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__proto__ vs. prototype example [duplicate]

This figure again shows that every object has a prototype. Constructor
function Foo also has its own __proto__ which is Function.prototype,
and which in turn also references via its __proto__ property again to
the Object.prototype. Thus, repeat, Foo.prototype is just an explicit
property of Foo which refers to the prototype of b and c objects.
var b = new Foo(20);
var c = new Foo(30);
What are the differences between __proto__ and prototype?
The figure was taken from dmitrysoshnikov.com.
Note: there is now a 2nd edition (2017) to the above 2010 article.

__proto__ is the actual object that is used in the lookup chain to resolve methods, etc. prototype is the object that is used to build __proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype
( new Foo ).prototype === undefined

prototype is a property of a Function object. It is the prototype of objects constructed by that function.
__proto__ is an internal property of an object, pointing to its prototype. Current standards provide an equivalent Object.getPrototypeOf(obj) method, though the de facto standard __proto__ is quicker.
You can find instanceof relationships by comparing a function's prototype to an object's __proto__ chain, and you can break these relationships by changing prototype.
function Point(x, y) {
this.x = x;
this.y = y;
}
var myPoint = new Point();
// the following are all true
myPoint.__proto__ == Point.prototype
myPoint.__proto__.__proto__ == Object.prototype
myPoint instanceof Point;
myPoint instanceof Object;
Here Point is a constructor function, it builds an object (data structure) procedurally. myPoint is an object constructed by Point() so Point.prototype gets saved to myPoint.__proto__ at that time.

prototype property is created when a function is declared.
For instance:
function Person(dob){
this.dob = dob
};
Person.prototype property is created internally once you declare above function.
Many properties can be added to the Person.prototype which are shared by Person instances created using new Person().
// adds a new method age to the Person.prototype Object.
Person.prototype.age = function(){return date-dob};
It is worth noting that Person.prototype is an Object literal by default (it can be changed as required).
Every instance created using new Person() has a __proto__ property which points to the Person.prototype. This is the chain that is used to traverse to find a property of a particular object.
var person1 = new Person(somedate);
var person2 = new Person(somedate);
creates 2 instances of Person, these 2 objects can call age method of Person.prototype as person1.age, person2.age.
In the above picture from your question, you can see that Foo is a Function Object and therefore it has a __proto__ link to the Function.prototype which in turn is an instance of Object and has a __proto__ link to Object.prototype. The proto link ends here with __proto__ in the Object.prototype pointing to null.
Any object can have access to all the properties in its proto chain as linked by __proto__ , thus forming the basis for prototypal inheritance.
__proto__ is not a standard way of accessing the prototype chain, the standard but similar approach is to use Object.getPrototypeOf(obj).
Below code for instanceof operator gives a better understanding:
object instanceof Class operator returns true when an object is an instance of a Class, more specifically if Class.prototype is found in the proto chain of that object then the object is an instance of that Class.
function instanceOf(Func){
var obj = this;
while(obj !== null){
if(Object.getPrototypeOf(obj) === Func.prototype)
return true;
obj = Object.getPrototypeOf(obj);
}
return false;
}
The above method can be called as: instanceOf.call(object, Class) which return true if object is instance of Class.

To explain let us create a function
function a (name) {
this.name = name;
}
When JavaScript executes this code, it adds prototype property to a, prototype property is an object with two properties to it:
constructor
__proto__
So when we do
a.prototype it returns
constructor: a // function definition
__proto__: Object
Now as you can see constructor is nothing but the function a itself
and __proto__ points to the root level Object of JavaScript.
Let us see what happens when we use a function with new key word.
var b = new a ('JavaScript');
When JavaScript executes this code it does 4 things:
It creates a new object, an empty object // {}
It creates __proto__ on b and makes it point to a.prototype so b.__proto__ === a.prototype
It executes a.prototype.constructor (which is definition of function a ) with the newly created object (created in step#1) as its context (this), hence the name property passed as 'JavaScript' (which is added to this) gets added to newly created object.
It returns newly created object in (created in step#1) so var b gets assigned to newly created object.
Now if we add a.prototype.car = "BMW" and do
b.car, the output "BMW" appears.
this is because when JavaScript executed this code it searched for car property on b, it did not find then JavaScript used b.__proto__ (which was made to point to 'a.prototype' in step#2) and finds car property so return "BMW".

A nice way to think of it is...
prototype is used by constructor functions. It should've really been called something like, "prototypeToInstall", since that's what it is.
and __proto__ is that "installed prototype" on an object (that was created/installed upon the object from said constructor() function)

Prototype VS. __proto__ VS. [[Prototype]]
When creating a function, a property object called prototype is being created automatically (you didn't create it yourself) and is being attached to the function object (the constructor). Note: This new prototype object also points to, or has an internal-private link to, the native JavaScript Object.
Example:
function Foo () {
this.name = 'John Doe';
}
// Foo has an object property called prototype.
// prototype was created automatically when we declared the function Foo.
Foo.hasOwnProperty('prototype'); // true
// Now, we can assign properties and methods to it:
Foo.prototype.myName = function () {
return 'My name is ' + this.name;
}
If you create a new object out of Foo using the new keyword, you are basically creating (among other things) a new object that has an internal or private link to the function Foo's prototype we discussed earlier:
var b = new Foo();
b.[[Prototype]] === Foo.prototype // true
The private linkage to that function's object called double brackets prototype or just [[Prototype]]. Many browsers are providing us a public linkage to it that called __proto__!
To be more specific, __proto__ is actually a getter function that belong to the native JavaScript Object. It returns the internal-private prototype linkage of whatever the this binding is (returns the [[Prototype]] of b):
b.__proto__ === Foo.prototype // true
It is worth noting that starting of ECMAScript5, you can also use the getPrototypeOf method to get the internal private linkage:
Object.getPrototypeOf(b) === b.__proto__ // true
NOTE: this answer doesn't intend to cover the whole process of creating new objects or new constructors, but to help better understand what is __proto__, prototype and [[Prototype]] and how it works.

To make it a little bit clear in addition to above great answers:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
eve.__proto__ == Person.prototype //true
eve.prototype //undefined
Instances have __proto__, classes have prototype.

In JavaScript, a function can be used as a constructor. That means we can create objects out of them using the new keyword. Every constructor function comes with a built-in object chained with them. This built-in object is called a prototype. Instances of a constructor function use __proto__ to access the prototype property of its constructor function.
First we created a constructor: function Foo(){}. To be clear, Foo is just another function. But we can create an object from it with the new keyword. That's why we call it the constructor function
Every function has a unique property which is called the prototype property. So, Constructor function Foo has a prototype property which points to its prototype, which is Foo.prototype (see image).
Constructor functions are themselves a function which is an instance of a system constructor called the [[Function]] constructor. So we can say that function Foo is constructed by a [[Function]] constructor. So, __proto__ of our Foo function will point to the prototype of its constructor, which is Function.prototype.
Function.prototype is itself is nothing but an object which is constructed from another system constructor called [[Object]]. So, [[Object]] is the constructor of Function.prototype. So, we can say Function.prototype is an instance of [[Object]]. So __proto__ of Function.prototype points to Object.prototype.
Object.prototype is the last man standing in the prototype chain. I mean it has not been constructed. It's already there in the system. So its __proto__ points to null.
Now we come to instances of Foo. When we create an instance using new Foo(), it creates a new object which is an instance of Foo. That means Foo is the constructor of these instances. Here we created two instances (x and y). __proto__ of x and y thus points to Foo.prototype.

I think you need to know the difference between __proto__ , [[prototype]] and prototype.
The accepted answer is helpful, but it might imply (imperfectly) that __proto__ is something only relevant to objects created using new on a constructor function, which is not true.
To be more precise: __proto__ exists on EVERY object.
But what is __proto__ at all?
Well, it is an object referencing another object which is also a property of all objects, called [[prototype]].
It's worth mentioning that [[prototype]] is something that JavaScript handles internally and is inaccessible to the developer.
Why would we need a reference object to the property [[prototype]] (of all objects)?
Because JavaScript doesn't want to allow getting / setting the [[prototype]] directly, so it allows it through a middle layer which is __proto__. So you can think of __proto__ as a getter/setter of the [[prototype]] property.
What is prototype then?
It is something specific to functions(Initially defined in Function, i.e, Function.prototype and then prototypically inherited by newly created functions, and then again those functions give it to their children, forming a chain of prototypical inheritance).
JavaScript uses a parent function's prototype to set its child functions' [[prototype]] when that parent function is run with new (remember we said all objects have [[prototype]]? well, functions are objects too, so they have [[prototype]] as well). So when the [[prototype]] of a function(child) is set to the prototype of another function(parent), you will have this in the end:
let child = new Parent();
child.__proto__ === Parent.prototype // --> true.
(Remember child.[[prototype]] is inaccessible, so we checked it using __proto__.)
Notice 1: Whenever a property is not in the child, its __proto__ will be searched "implicitly". So for instance, if child.myprop returns a value, you can't say whether "myprop" was a property of the child, or of one of its parents' prototypes. This also means that you never need to do something like: child.__proto__.__proto__.myprop on your own, just child.myprop will do that for you automatically.
Notice 2: Even if the parent's prototype has items in it, the child's own prototype will be an empty object initially. You can add items to it or remove from it manually though, if you want to further extend the inhertance chain(add child[ren] to the child). Or it can be manipulated implicitly, e.g., using the class syntax.)
Notice 3: In case you need to set/get the [[prototype]] yourself, using __proto__ is a bit outdated and modern JavaScript suggests using Object.setPrototypeOf and Object.getPrototypeOf instead.

Summary:
The __proto__ property of an object is a property that maps to the prototype of the constructor function of the object. In other words:
instance.__proto__ === constructor.prototype // true
This is used to form the prototype chain of an object. The prototype chain is a lookup mechanism for properties on an object. If an object's property is accessed, JavaScript will first look on the object itself. If the property isn't found there, it will climb all the way up to protochain until it is found (or not)
Example:
function Person (name, city) {
this.name = name;
}
Person.prototype.age = 25;
const willem = new Person('Willem');
console.log(willem.__proto__ === Person.prototype); // the __proto__ property on the instance refers to the prototype of the constructor
console.log(willem.age); // 25 doesn't find it at willem object but is present at prototype
console.log(willem.__proto__.age); // now we are directly accessing the prototype of the Person function
Our first log results to true, this is because as mentioned the __proto__ property of the instance created by the constructor refers to the prototype property of the constructor. Remember, in JavaScript, functions are also Objects. Objects can have properties, and a default property of any function is one property named prototype.
Then, when this function is utilized as a constructor function, the object instantiated from it will receive a property called __proto__. And this __proto__ property refers to the prototype property of the constructor function (which by default every function has).
Why is this useful?
JavaScript has a mechanism when looking up properties on Objects which is called 'prototypal inheritance', here is what it basically does:
First, it's checked if the property is located on the Object itself. If so, this property is returned.
If the property is not located on the object itself, it will 'climb up the protochain'. It basically looks at the object referred to by the __proto__ property. There, it checks if the property is available on the object referred to by __proto__.
If the property isn't located on the __proto__ object, it will climb up the __proto__ chain, all the way up to Object object.
If it cannot find the property anywhere on the object and its prototype chain, it will return undefined.
For example:
function Person (name) {
this.name = name;
}
let mySelf = new Person('Willem');
console.log(mySelf.__proto__ === Person.prototype);
console.log(mySelf.__proto__.__proto__ === Object.prototype);

'use strict'
function A() {}
var a = new A();
class B extends A {}
var b = new B();
console.log('====='); // =====
console.log(B.__proto__ === A); // true
console.log(B.prototype.__proto__ === A.prototype); // true
console.log(b.__proto__ === B.prototype); // true
console.log(a.__proto__ === A.prototype); // true
console.log(A.__proto__ === Function.__proto__); // true
console.log(Object.__proto__ === Function.__proto__); // true
console.log(Object.prototype === Function.__proto__.__proto__); // true
console.log(Object.prototype.__proto__ === null); // true
In JavaScript, Every object(function is object too!) has a __proto__ property, the property is reference to its prototype.
When we use the new operator with a constructor to create a new object,
the new object's __proto__ property will be set with constructor's prototype property,
then the constructor will be call by the new object,
in that process "this" will be a reference to the new object in the constructor scope, finally return the new object.
Constructor's prototype is __proto__ property, Constructor's prototype property is work with the new operator.
Constructor must be a function, but function not always is constructor even if it has prototype property.
Prototype chain actually is object's __proto__ property to reference its prototype,
and the prototype's __proto__ property to reference the prototype's prototype, and so on,
until to reference Object's prototype's __proto__ property which is reference to null.
For example:
console.log(a.constructor === A); // true
// "a" don't have constructor,
// so it reference to A.prototype by its ``__proto__`` property,
// and found constructor is reference to A
[[Prototype]] and __proto__ property actually is same thing.
We can use Object's getPrototypeOf method to get something's prototype.
console.log(Object.getPrototypeOf(a) === a.__proto__); // true
Any function we written can be use to create an object with the new operator,
so anyone of those functions can be a constructor.

I happen to be learning prototype from You Don't Know JS: this & Object Prototypes, which is a wonderful book to understand the design underneath and clarify so many misconceptions (that's why I'm trying to avoid using inheritance and things like instanceof).
But I have the same question as people asked here. Several answers are really helpful and enlightening. I'd also love to share my understandings.
What is a prototype?
Objects in JavaScript have an internal property, denoted in the specification as[[Prototype]], which is simply a reference to another object. Almost all objects are given a non-nullvalue for this property, at the time of their creation.
How to get an object's prototype?
via __proto__or Object.getPrototypeOf
var a = { name: "wendi" };
a.__proto__ === Object.prototype // true
Object.getPrototypeOf(a) === Object.prototype // true
function Foo() {};
var b = new Foo();
b.__proto__ === Foo.prototype
b.__proto__.__proto__ === Object.prototype
What is the prototype ?
prototype is an object automatically created as a special property of a function, which is used to establish the delegation (inheritance) chain, aka prototype chain.
When we create a function a, prototype is automatically created as a special property on a and saves the function code on as the constructor on prototype.
function Foo() {};
Foo.prototype // Object {constructor: function}
Foo.prototype.constructor === Foo // true
I'd love to consider this property as the place to store the properties (including methods) of a function object. That's also the reason why utility functions in JS are defined like Array.prototype.forEach() , Function.prototype.bind(), Object.prototype.toString().
Why to emphasize the property of a function?
{}.prototype // undefined;
(function(){}).prototype // Object {constructor: function}
// The example above shows object does not have the prototype property.
// But we have Object.prototype, which implies an interesting fact that
typeof Object === "function"
var obj = new Object();
So, Arary, Function, Objectare all functions. I should admit that this refreshes my impression on JS. I know functions are first-class citizen in JS but it seems that it is built on functions.
What's the difference between __proto__ and prototype?
__proto__a reference works on every object to refer to its [[Prototype]]property.
prototype is an object automatically created as a special property of a function, which is used to store the properties (including methods) of a function object.
With these two, we could mentally map out the prototype chain. Like this picture illustrates:
function Foo() {}
var b = new Foo();
b.__proto__ === Foo.prototype // true
Foo.__proto__ === Function.prototype // true
Function.prototype.__proto__ === Object.prototype // true

I know, I am late but let me try to simplify it.
Let us say there is a function
function Foo(message){
this.message = message ;
};
console.log(Foo.prototype);
Foo function will have a prototype object linked. So,Whenever we create a function in JavaScript, it always has a prototype object linked to it.
Now let us go ahead and create two objects using the function Foo.
var a = new Foo("a");
var b = new Foo("b");
console.log(a.message);
console.log(b.message);
Now we have two objects, object a and object b. Both are created
using constructor Foo. Keep in mind constructor is just a word here.
Object a and b both have a copy of message property.
These two objects a and b are linked to prototype object of constructor Foo.
On objects a and b, we can access Foo prototype using __proto__ property in all browsers and in IE we can use Object.getPrototypeOf(a) or Object.getPrototypeOf(b)
Now, Foo.prototype, a.__proto__, and b.__proto__ all denotes same object.
b.__proto__ === Object.getPrototypeOf(a);
a.__proto__ === Foo.prototype;
a.constructor.prototype === a.__proto__;
all of above would return true.
As we know, in JavaScript properties can be added dynamically. We can add property to object
Foo.prototype.Greet = function(){
console.log(this.message);
}
a.Greet();//a
b.Greet();//b
a.constructor.prototype.Greet();//undefined
As you see we added Greet() method in Foo.prototype but it is accessible in a and b or any other object which is constructed using Foo.
While executing a.Greet(), JavaScript will first search Greet in object a on property list. On not finding , it will go up in __proto__ chain of a. Since a.__proto__ and Foo.prototype is same object, JavaScript will find Greet() method and execute it.
I hope, now prototype and __proto__ is simplified a bit.

Another good way to understand it:
var foo = {}
/*
foo.constructor is Object, so foo.constructor.prototype is actually
Object.prototype; Object.prototype in return is what foo.__proto__ links to.
*/
console.log(foo.constructor.prototype === foo.__proto__);
// this proves what the above comment proclaims: Both statements evaluate to true.
console.log(foo.__proto__ === Object.prototype);
console.log(foo.constructor.prototype === Object.prototype);
Only after IE11 __proto__ is supported. Before that version, such as IE9, you could use the constructor to get the __proto__.

prototype
prototype is a property of a Function. It is the blueprint for creating objects by using that (constructor) function with new keyword.
__proto__
__proto__ is used in the lookup chain to resolve methods, properties. when an object is created (using constructor function with new keyword), __proto__ is set to (Constructor) Function.prototype
function Robot(name) {
this.name = name;
}
var robot = new Robot();
// the following are true
robot.__proto__ == Robot.prototype
robot.__proto__.__proto__ == Object.prototype
Here is my (imaginary) explanation to clear the confusion:
Imagine there is an imaginary class (blueprint/coockie cutter) associated with function. That imaginary class is used to instantiate objects. prototype is the extention mechanism (extention method in C#, or Swift Extension) to add things to that imaginary class.
function Robot(name) {
this.name = name;
}
The above can be imagined as:
// imaginary class
class Robot extends Object{
static prototype = Robot.class
// Robot.prototype is the way to add things to Robot class
// since Robot extends Object, therefore Robot.prototype.__proto__ == Object.prototype
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
}
So,
var robot = new Robot();
robot.__proto__ == Robot.prototype
robot.prototype == undefined
robot.__proto__.__proto__ == Object.prototype
Now adding method to the prototype of Robot:
Robot.prototype.move(x, y) = function(x, y){ Robot.position.x = x; Robot.position.y = y};
// Robot.prototype.move(x, y) ===(imagining)===> Robot.class.move(x, y)
The above can be imagined as extension of Robot class:
// Swift way of extention
extension Robot{
function move(x, y){
Robot.position.x = x; Robot.position.y = y
}
}
Which in turn,
// imaginary class
class Robot{
static prototype = Robot.class // Robot.prototype way to extend Robot class
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
// added by prototype (as like C# extension method)
function move(x, y){
Robot.position.x = x; Robot.position.y = y
};
}

I've made for myself a small drawing that represents the following code snippet:
var Cat = function() {}
var tom = new Cat()
I have a classical OO background, so it was helpful to represent the hierarchy in this manner. To help you read this diagram, treat the rectangles in the image as JavaScript objects. And yes, functions are also objects. ;)
Objects in JavaScript have properties and __proto__ is just one of them.
The idea behind this property is to point to the ancestor object in the (inheritance) hierarchy.
The root object in JavaScript is Object.prototype and all other objects are descendants of this one. The __proto__ property of the root object is null, which represents the end of inheritance chain.
You'll notice that prototype is a property of functions. Cat is a function, but also Function and Object are (native) functions. tom is not a function, thus it does not have this property.
The idea behind this property is to point to an object which will be used in the construction, i.e. when you call the new operator on that function.
Note that prototype objects (yellow rectangles) have another property called
constructor which points back to the respective function object. For
brevity reasons this was not depicted.
Indeed, when we create the tom object with new Cat(), the created object will have the __proto__ property set to the prototype object of the constructor function.
In the end, let us play with this diagram a bit. The following statements are true:
tom.__proto__ property points to the same object as Cat.prototype.
Cat.__proto__ points to the Function.prototype object, just like Function.__proto__ and Object.__proto__ do.
Cat.prototype.__proto__ and tom.__proto__.__proto__ point to the same object and that is Object.prototype.
Cheers!

[[Prototype]] :
[[Prototype]] is an internal hidden property of objects in JS and it is a reference to another object. Every object at the time of creation receives a non-null value for [[Prototype]]. Remember [[Get]] operation is invoked when we reference a property on an object like, myObject.a. If the object itself has a property, a on it then that property will be used.
let myObject= {
a: 2
};
console.log(myObject.a); // 2
But if the object itself directly does not have the requested property then [[Get]] operation will proceed to follow the [[Prototype]] link of the object. This process will continue until either a matching property name is found or the [[Prototype]] chain ends(at the built-in Object.prototype). If no matching property is found then undefined will be returned. Object.create(specifiedObject) creates an object with the [[Prototype]] linkage to the specified object.
let anotherObject= {
a: 2
};
// create an object linked to anotherObject
let myObject= Object.create(anotherObject);
console.log(myObject.a); // 2
Both for..in loop and in operator use [[Prototype]] chain lookup process. So if we use for..in loop to iterate over the properties of an object then all the enumerable properties which can be reached via that object's [[Prototype]] chain also will be enumerated along with the enumerable properties of the object itself. And when using in operator to test for the existence of a property on an object then in operator will check all the properties via [[Prototype]] linkage of the object regardless of their enumerability.
// for..in loop uses [[Prototype]] chain lookup process
let anotherObject= {
a: 2
};
let myObject= Object.create(anotherObject);
for(let k in myObject) {
console.log("found: " + k); // found: a
}
// in operator uses [[Prototype]] chain lookup process
console.log("a" in myObject); // true
.prototype :
.prototype is a property of functions in JS and it refers to an object having constructor property which stores all the properties(and methods) of the function object.
let foo= function(){}
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties
foo.id= "Walter White";
foo.job= "teacher";
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties and 2 more properties that we added to the fn object
/*
{constructor: f}
constructor: f()
id: "Walter White"
job: "teacher"
arguments: null
caller: null
length: 0
name: "foo"
prototype: {constructor: f}
__proto__: f()
[[FunctionLocation]]: VM789:1
[[Scopes]]: Scopes[2]
__proto__: Object
*/
But normal objects in JS does not have .prototype property. We know Object.prototype is the root object of all the objects in JS. So clearly Object is a function i.e. typeof Object === "function" . That means we also can create object from the Object function like, let myObj= new Object( ). Similarly Array, Function are also functions so we can use Array.prototype, Function.prototype to store all the generic properties of arrays and functions. So we can say JS is built on functions.
{}.prototype; // SyntaxError: Unexpected token '.'
(function(){}).prototype; // {constructor: f}
Also using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. In the below code, we have created an object, a from a fn, Letter and added 2 properties one to the fn object and another to the prototype object of the fn. Now if we try to access both of the properties on the newly created object, a then we only will be able to access the property added to the prototype object of the function. This is because the prototype object of the function is now on the [[Prototype]] chain of the newly created object, a.
let Letter= function(){}
let a= new Letter();
Letter.from= "Albuquerque";
Letter.prototype.to= "New Hampshire";
console.log(a.from); // undefined
console.log(a.to); // New Hampshire
.__proto__ :
.__proto__ is a property of objects in JS and it references the another object in the [[Prototype]] chain. We know [[Prototype]] is an internal hidden property of objects in JS and it references another object in the [[Prototype]] chain. We can get or set the object referred by the internal [[Prototype]] property in 2 ways
Object.getPrototypeOf(obj) / Object.setPrototypeOf(obj)
obj.__proto__
We can traverse the [[Prototype]] chain using: .__proto__.__proto__. . . Along with .constructor, .toString( ), .isPrototypeOf( ) our dunder proto property (__proto__) actually exists on the built-in Object.prototype root object, but available on any particular object. Our .__proto__ is actually a getter/setter. Implementation of .__proto__ in Object.prototype is as below :
Object.defineProperty(Object.prototype, "__proto__", {
get: function() {
return Object.getPrototypeOf(this);
},
set: function(o) {
Object.setPrototypeOf(this, o);
return o;
}
});
To retrieve the value of obj.__proto__ is like calling, obj.__proto__() which actually returns the calling of the getter fn, Object.getPrototypeOf(obj) which exists on Object.prototype object. Although .__proto__ is a settable property but we should not change [[Prototype]] of an already existing object because of performance issues.
Using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. Using .__proto__ property we can access the other object referenced by internal hidden [[Prototype]] property of the object. But __proto__ is not the same as [[Prototype]] rather a getter/setter for it. Consider below code :
let Letter= function() {}
let a= new Letter();
let b= new Letter();
let z= new Letter();
// output in console
a.__proto__ === Letter.prototype; // true
b.__proto__ === Letter.prototype; // true
z.__proto__ === Letter.prototype; // true
Letter.__proto__ === Function.prototype; // true
Function.prototype.__proto__ === Object.prototype; // true
Letter.prototype.__proto__ === Object.prototype; // true

To put it simply:
> var a = 1
undefined
> a.__proto__
[Number: 0]
> Number.prototype
[Number: 0]
> Number.prototype === a.__proto__
true
This allows you to attach properties to X.prototype AFTER objects of type X has been instantiated, and they will still get access to those new properties through the __proto__ reference which the Javascript-engine uses to walk up the prototype chain.

Prototype or Object.prototype is a property of an object literal. It represents the Object prototype object which you can override to add more properties or methods further along the prototype chain.
__proto__ is an accessor property (get and set function) that exposes the internal prototype of an object thru which it is accessed.
References:
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/prototype
http://www.w3schools.com/js/js_object_prototypes.asp
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/proto

Explanatory example:
function Dog(){}
Dog.prototype.bark = "woof"
let myPuppie = new Dog()
now, myPupppie has __proto__ property which points to Dog.prototype.
> myPuppie.__proto__
>> {bark: "woof", constructor: ƒ}
but myPuppie does NOT have a prototype property.
> myPuppie.prototype
>> undefined
So, __proto__ of mypuppie is the reference to the .prototype property of constructor function that was used to instantiate this object (and the current myPuppie object has "delegates to" relationship to this __proto__ object), while .prototype property of myPuppie is simply absent (since we did not set it).
Good explanation by MPJ here:
proto vs prototype - Object Creation in JavaScript

DEFINITIONS
(number inside the parenthesis () is a 'link' to the code that is written below)
prototype - an object that consists of:
=> functions (3) of this
particular ConstructorFunction.prototype(5) that are accessible by each
object (4) created or to-be-created through this constructor function (1)
=> the constructor function itself (1)
=> __proto__ of this particular object (prototype object)
__proto__ (dandor proto?) - a link BETWEEN any object (2) created through a particular constructor function (1), AND the prototype object's properties (5) of that constructor THAT allows each created object (2) to have access to the prototype's functions and methods (4) (__proto__ is by default included in every single object in JS)
CODE CLARIFICATION
1.
function Person (name, age) {
this.name = name;
this.age = age;
}
2.
var John = new Person(‘John’, 37);
// John is an object
3.
Person.prototype.getOlder = function() {
this.age++;
}
// getOlder is a key that has a value of the function
4.
John.getOlder();
5.
Person.prototype;

I'll try a 4th grade explanation:
Things are very simple. A prototype is an example of how something should be built. So:
I'm a function and I build new objects similar to my prototype
I'm an object and I was built using my __proto__ as an example
proof:
function Foo() { }
var bar = new Foo()
// `bar` is constructed from how Foo knows to construct objects
bar.__proto__ === Foo.prototype // => true
// bar is an instance - it does not know how to create objects
bar.prototype // => undefined

Every function you create has a property called prototype, and it starts off its life as an empty object. This property is of no use until you use this function as constructor function i.e. with the 'new' keyword.
This is often confused with the __proto__ property of an object. Some might get confused and except that the prototype property of an object might get them the proto of an object. But this is not case. prototype is used to get the __proto__ of an object created from a function constructor.
In the above example:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
console.log(eve.__proto__ == Person.prototype) // true
// this is exactly what prototype does, made Person.prototype equal to eve.__proto__
I hope it makes sense.

What about using __proto__ for static methods?
function Foo(name){
this.name = name
Foo.__proto__.collection.push(this)
Foo.__proto__.count++
}
Foo.__proto__.count=0
Foo.__proto__.collection=[]
var bar = new Foo('bar')
var baz = new Foo('baz')
Foo.count;//2
Foo.collection // [{...}, {...}]
bar.count // undefined

(function(){
let a = function(){console.log(this.b)};
a.prototype.b = 1;
a.__proto__.b = 2;
let q = new a();
console.log(a.b);
console.log(q.b)
})()
Try this code to understand

There is only one object that is used for protypal chaining. This object obviously has a name and a value: __proto__ is its name, and prototype is its value. That's all.
to make it even easier to grasp, look at the diagram on the top of this post (Diagram by dmitry soshnikov), you'll never find __proto__ points to something else other than prototype as its value.
The gist is this: __proto__ is the name that references the prototypal object, and prototype is the actual prototypal object.
It's like saying:
let x = {name: 'john'};
x is the object name (pointer), and {name: 'john'} is the actual object (data value).
NOTE: this just a massively simplified hint on how they are related on a high level.
Update: Here is a simple concrete javascript example for better illustration:
let x = new String("testing") // Or any other javascript object you want to create
Object.getPrototypeOf(x) === x.__proto__; // true
This means that when Object.getPrototypeOf(x) gets us the actual value of x (which is its prototype), is exactly what the __proto__ of x is pointing to. Therefore __proto__ is indeed pointing to the prototype of x. Thus __proto__ references x (pointer of x), and prototype is the value of x (its prototype).
I hope it's a bit clear now.

so many good answers exist for this question, but for recap and compact form of answer that have good details I add the following:
the first thing that we must consider is when JS was invented, computers have very low memory, so if we need a process for creating new object types, we must consider memory performance.
so they located methods that object created from that specific object type need, on the separate part of memory instead of every time we create a new object, store methods besides the object.
so if we reinvent the new operator and constructor function concept with JS's new features we have these steps:
and empty object. (that will be the final result of instantiation of object type)
let empty={}
we already know that for memory performance reasons all the methods that are needed for instances of an object type are located on the constructor function's prototype property. (functions are also objects so they can have properties)
so we reference the empty object's __protp__ to the location where those methods exist.
(we consider the function that we use conceptually as the constructor, named constructor.
empty.__proto__ = constructor.prototype
we must initialize object type values.
in JS function are disconnected from objects. with dot notation or methods like bind call apply that function objects have we must tell "what is the this context of the function".
let newFunc = constructor.bind(empty)
now we have a new function that has an empty object as this context.
after execution of this function. the empty object will be filled, and the result of instantiation of type object will be this empty object if defined constructor function doesn't return(as if that will be the result of the process)
so as you see __proto__ is a property of objects that refers to other objects(in JS functions are also object) prototype object property which consisted of properties that use across instances of a specific object type.
as you can guess from the phrase, functions are objects, functions also have __proto__ property so they can refer to other object's prototype properties. this is how prototype inheritance is implemented.

my understanding is: __proto__ and prototype are all served for the prototype chain technique . the difference is functions named with underscore(like __proto__) are not aim for developers invoked explicitly at all. in other words, they are just for some mechanisms like inherit etc. they are 'back-end'. but functions named without underscore are designed for invoked explicitly, they are 'front-end'.

__proto__ is the base to construct prototype and a constructor function eg: function human(){} has prototype which is shared via __proto__ in the new instance of the constructor function. A more detailed read here

As this rightly stated
__proto__ is the actual object that is used in the lookup chain to
resolve methods, etc. prototype is the object that is used to build
__proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype;
( new Foo ).prototype === undefined;
We can further note that __proto__ property of an object created using function constructor points towards the memory location pointed towards by prototype property of that respective constructor.
If we change the memory location of prototype of constructor function, __proto__ of derived object will still continue to point towards the original address space. Therefore to make common property available down the inheritance chain, always append property to constructor function prototype, instead of re-initializing it (which would change its memory address).
Consider the following example:
function Human(){
this.speed = 25;
}
var himansh = new Human();
Human.prototype.showSpeed = function(){
return this.speed;
}
himansh.__proto__ === Human.prototype; //true
himansh.showSpeed(); //25
//now re-initialzing the Human.prototype aka changing its memory location
Human.prototype = {lhs: 2, rhs:3}
//himansh.__proto__ will still continue to point towards the same original memory location.
himansh.__proto__ === Human.prototype; //false
himansh.showSpeed(); //25

Object created from new keyword doesn't have prototype in JavaScript? [duplicate]

This figure again shows that every object has a prototype. Constructor
function Foo also has its own __proto__ which is Function.prototype,
and which in turn also references via its __proto__ property again to
the Object.prototype. Thus, repeat, Foo.prototype is just an explicit
property of Foo which refers to the prototype of b and c objects.
var b = new Foo(20);
var c = new Foo(30);
What are the differences between __proto__ and prototype?
The figure was taken from dmitrysoshnikov.com.
Note: there is now a 2nd edition (2017) to the above 2010 article.

__proto__ is the actual object that is used in the lookup chain to resolve methods, etc. prototype is the object that is used to build __proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype
( new Foo ).prototype === undefined

prototype is a property of a Function object. It is the prototype of objects constructed by that function.
__proto__ is an internal property of an object, pointing to its prototype. Current standards provide an equivalent Object.getPrototypeOf(obj) method, though the de facto standard __proto__ is quicker.
You can find instanceof relationships by comparing a function's prototype to an object's __proto__ chain, and you can break these relationships by changing prototype.
function Point(x, y) {
this.x = x;
this.y = y;
}
var myPoint = new Point();
// the following are all true
myPoint.__proto__ == Point.prototype
myPoint.__proto__.__proto__ == Object.prototype
myPoint instanceof Point;
myPoint instanceof Object;
Here Point is a constructor function, it builds an object (data structure) procedurally. myPoint is an object constructed by Point() so Point.prototype gets saved to myPoint.__proto__ at that time.

prototype property is created when a function is declared.
For instance:
function Person(dob){
this.dob = dob
};
Person.prototype property is created internally once you declare above function.
Many properties can be added to the Person.prototype which are shared by Person instances created using new Person().
// adds a new method age to the Person.prototype Object.
Person.prototype.age = function(){return date-dob};
It is worth noting that Person.prototype is an Object literal by default (it can be changed as required).
Every instance created using new Person() has a __proto__ property which points to the Person.prototype. This is the chain that is used to traverse to find a property of a particular object.
var person1 = new Person(somedate);
var person2 = new Person(somedate);
creates 2 instances of Person, these 2 objects can call age method of Person.prototype as person1.age, person2.age.
In the above picture from your question, you can see that Foo is a Function Object and therefore it has a __proto__ link to the Function.prototype which in turn is an instance of Object and has a __proto__ link to Object.prototype. The proto link ends here with __proto__ in the Object.prototype pointing to null.
Any object can have access to all the properties in its proto chain as linked by __proto__ , thus forming the basis for prototypal inheritance.
__proto__ is not a standard way of accessing the prototype chain, the standard but similar approach is to use Object.getPrototypeOf(obj).
Below code for instanceof operator gives a better understanding:
object instanceof Class operator returns true when an object is an instance of a Class, more specifically if Class.prototype is found in the proto chain of that object then the object is an instance of that Class.
function instanceOf(Func){
var obj = this;
while(obj !== null){
if(Object.getPrototypeOf(obj) === Func.prototype)
return true;
obj = Object.getPrototypeOf(obj);
}
return false;
}
The above method can be called as: instanceOf.call(object, Class) which return true if object is instance of Class.

To explain let us create a function
function a (name) {
this.name = name;
}
When JavaScript executes this code, it adds prototype property to a, prototype property is an object with two properties to it:
constructor
__proto__
So when we do
a.prototype it returns
constructor: a // function definition
__proto__: Object
Now as you can see constructor is nothing but the function a itself
and __proto__ points to the root level Object of JavaScript.
Let us see what happens when we use a function with new key word.
var b = new a ('JavaScript');
When JavaScript executes this code it does 4 things:
It creates a new object, an empty object // {}
It creates __proto__ on b and makes it point to a.prototype so b.__proto__ === a.prototype
It executes a.prototype.constructor (which is definition of function a ) with the newly created object (created in step#1) as its context (this), hence the name property passed as 'JavaScript' (which is added to this) gets added to newly created object.
It returns newly created object in (created in step#1) so var b gets assigned to newly created object.
Now if we add a.prototype.car = "BMW" and do
b.car, the output "BMW" appears.
this is because when JavaScript executed this code it searched for car property on b, it did not find then JavaScript used b.__proto__ (which was made to point to 'a.prototype' in step#2) and finds car property so return "BMW".

A nice way to think of it is...
prototype is used by constructor functions. It should've really been called something like, "prototypeToInstall", since that's what it is.
and __proto__ is that "installed prototype" on an object (that was created/installed upon the object from said constructor() function)

Prototype VS. __proto__ VS. [[Prototype]]
When creating a function, a property object called prototype is being created automatically (you didn't create it yourself) and is being attached to the function object (the constructor). Note: This new prototype object also points to, or has an internal-private link to, the native JavaScript Object.
Example:
function Foo () {
this.name = 'John Doe';
}
// Foo has an object property called prototype.
// prototype was created automatically when we declared the function Foo.
Foo.hasOwnProperty('prototype'); // true
// Now, we can assign properties and methods to it:
Foo.prototype.myName = function () {
return 'My name is ' + this.name;
}
If you create a new object out of Foo using the new keyword, you are basically creating (among other things) a new object that has an internal or private link to the function Foo's prototype we discussed earlier:
var b = new Foo();
b.[[Prototype]] === Foo.prototype // true
The private linkage to that function's object called double brackets prototype or just [[Prototype]]. Many browsers are providing us a public linkage to it that called __proto__!
To be more specific, __proto__ is actually a getter function that belong to the native JavaScript Object. It returns the internal-private prototype linkage of whatever the this binding is (returns the [[Prototype]] of b):
b.__proto__ === Foo.prototype // true
It is worth noting that starting of ECMAScript5, you can also use the getPrototypeOf method to get the internal private linkage:
Object.getPrototypeOf(b) === b.__proto__ // true
NOTE: this answer doesn't intend to cover the whole process of creating new objects or new constructors, but to help better understand what is __proto__, prototype and [[Prototype]] and how it works.

To make it a little bit clear in addition to above great answers:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
eve.__proto__ == Person.prototype //true
eve.prototype //undefined
Instances have __proto__, classes have prototype.

In JavaScript, a function can be used as a constructor. That means we can create objects out of them using the new keyword. Every constructor function comes with a built-in object chained with them. This built-in object is called a prototype. Instances of a constructor function use __proto__ to access the prototype property of its constructor function.
First we created a constructor: function Foo(){}. To be clear, Foo is just another function. But we can create an object from it with the new keyword. That's why we call it the constructor function
Every function has a unique property which is called the prototype property. So, Constructor function Foo has a prototype property which points to its prototype, which is Foo.prototype (see image).
Constructor functions are themselves a function which is an instance of a system constructor called the [[Function]] constructor. So we can say that function Foo is constructed by a [[Function]] constructor. So, __proto__ of our Foo function will point to the prototype of its constructor, which is Function.prototype.
Function.prototype is itself is nothing but an object which is constructed from another system constructor called [[Object]]. So, [[Object]] is the constructor of Function.prototype. So, we can say Function.prototype is an instance of [[Object]]. So __proto__ of Function.prototype points to Object.prototype.
Object.prototype is the last man standing in the prototype chain. I mean it has not been constructed. It's already there in the system. So its __proto__ points to null.
Now we come to instances of Foo. When we create an instance using new Foo(), it creates a new object which is an instance of Foo. That means Foo is the constructor of these instances. Here we created two instances (x and y). __proto__ of x and y thus points to Foo.prototype.

I think you need to know the difference between __proto__ , [[prototype]] and prototype.
The accepted answer is helpful, but it might imply (imperfectly) that __proto__ is something only relevant to objects created using new on a constructor function, which is not true.
To be more precise: __proto__ exists on EVERY object.
But what is __proto__ at all?
Well, it is an object referencing another object which is also a property of all objects, called [[prototype]].
It's worth mentioning that [[prototype]] is something that JavaScript handles internally and is inaccessible to the developer.
Why would we need a reference object to the property [[prototype]] (of all objects)?
Because JavaScript doesn't want to allow getting / setting the [[prototype]] directly, so it allows it through a middle layer which is __proto__. So you can think of __proto__ as a getter/setter of the [[prototype]] property.
What is prototype then?
It is something specific to functions(Initially defined in Function, i.e, Function.prototype and then prototypically inherited by newly created functions, and then again those functions give it to their children, forming a chain of prototypical inheritance).
JavaScript uses a parent function's prototype to set its child functions' [[prototype]] when that parent function is run with new (remember we said all objects have [[prototype]]? well, functions are objects too, so they have [[prototype]] as well). So when the [[prototype]] of a function(child) is set to the prototype of another function(parent), you will have this in the end:
let child = new Parent();
child.__proto__ === Parent.prototype // --> true.
(Remember child.[[prototype]] is inaccessible, so we checked it using __proto__.)
Notice 1: Whenever a property is not in the child, its __proto__ will be searched "implicitly". So for instance, if child.myprop returns a value, you can't say whether "myprop" was a property of the child, or of one of its parents' prototypes. This also means that you never need to do something like: child.__proto__.__proto__.myprop on your own, just child.myprop will do that for you automatically.
Notice 2: Even if the parent's prototype has items in it, the child's own prototype will be an empty object initially. You can add items to it or remove from it manually though, if you want to further extend the inhertance chain(add child[ren] to the child). Or it can be manipulated implicitly, e.g., using the class syntax.)
Notice 3: In case you need to set/get the [[prototype]] yourself, using __proto__ is a bit outdated and modern JavaScript suggests using Object.setPrototypeOf and Object.getPrototypeOf instead.

Summary:
The __proto__ property of an object is a property that maps to the prototype of the constructor function of the object. In other words:
instance.__proto__ === constructor.prototype // true
This is used to form the prototype chain of an object. The prototype chain is a lookup mechanism for properties on an object. If an object's property is accessed, JavaScript will first look on the object itself. If the property isn't found there, it will climb all the way up to protochain until it is found (or not)
Example:
function Person (name, city) {
this.name = name;
}
Person.prototype.age = 25;
const willem = new Person('Willem');
console.log(willem.__proto__ === Person.prototype); // the __proto__ property on the instance refers to the prototype of the constructor
console.log(willem.age); // 25 doesn't find it at willem object but is present at prototype
console.log(willem.__proto__.age); // now we are directly accessing the prototype of the Person function
Our first log results to true, this is because as mentioned the __proto__ property of the instance created by the constructor refers to the prototype property of the constructor. Remember, in JavaScript, functions are also Objects. Objects can have properties, and a default property of any function is one property named prototype.
Then, when this function is utilized as a constructor function, the object instantiated from it will receive a property called __proto__. And this __proto__ property refers to the prototype property of the constructor function (which by default every function has).
Why is this useful?
JavaScript has a mechanism when looking up properties on Objects which is called 'prototypal inheritance', here is what it basically does:
First, it's checked if the property is located on the Object itself. If so, this property is returned.
If the property is not located on the object itself, it will 'climb up the protochain'. It basically looks at the object referred to by the __proto__ property. There, it checks if the property is available on the object referred to by __proto__.
If the property isn't located on the __proto__ object, it will climb up the __proto__ chain, all the way up to Object object.
If it cannot find the property anywhere on the object and its prototype chain, it will return undefined.
For example:
function Person (name) {
this.name = name;
}
let mySelf = new Person('Willem');
console.log(mySelf.__proto__ === Person.prototype);
console.log(mySelf.__proto__.__proto__ === Object.prototype);

'use strict'
function A() {}
var a = new A();
class B extends A {}
var b = new B();
console.log('====='); // =====
console.log(B.__proto__ === A); // true
console.log(B.prototype.__proto__ === A.prototype); // true
console.log(b.__proto__ === B.prototype); // true
console.log(a.__proto__ === A.prototype); // true
console.log(A.__proto__ === Function.__proto__); // true
console.log(Object.__proto__ === Function.__proto__); // true
console.log(Object.prototype === Function.__proto__.__proto__); // true
console.log(Object.prototype.__proto__ === null); // true
In JavaScript, Every object(function is object too!) has a __proto__ property, the property is reference to its prototype.
When we use the new operator with a constructor to create a new object,
the new object's __proto__ property will be set with constructor's prototype property,
then the constructor will be call by the new object,
in that process "this" will be a reference to the new object in the constructor scope, finally return the new object.
Constructor's prototype is __proto__ property, Constructor's prototype property is work with the new operator.
Constructor must be a function, but function not always is constructor even if it has prototype property.
Prototype chain actually is object's __proto__ property to reference its prototype,
and the prototype's __proto__ property to reference the prototype's prototype, and so on,
until to reference Object's prototype's __proto__ property which is reference to null.
For example:
console.log(a.constructor === A); // true
// "a" don't have constructor,
// so it reference to A.prototype by its ``__proto__`` property,
// and found constructor is reference to A
[[Prototype]] and __proto__ property actually is same thing.
We can use Object's getPrototypeOf method to get something's prototype.
console.log(Object.getPrototypeOf(a) === a.__proto__); // true
Any function we written can be use to create an object with the new operator,
so anyone of those functions can be a constructor.

I happen to be learning prototype from You Don't Know JS: this & Object Prototypes, which is a wonderful book to understand the design underneath and clarify so many misconceptions (that's why I'm trying to avoid using inheritance and things like instanceof).
But I have the same question as people asked here. Several answers are really helpful and enlightening. I'd also love to share my understandings.
What is a prototype?
Objects in JavaScript have an internal property, denoted in the specification as[[Prototype]], which is simply a reference to another object. Almost all objects are given a non-nullvalue for this property, at the time of their creation.
How to get an object's prototype?
via __proto__or Object.getPrototypeOf
var a = { name: "wendi" };
a.__proto__ === Object.prototype // true
Object.getPrototypeOf(a) === Object.prototype // true
function Foo() {};
var b = new Foo();
b.__proto__ === Foo.prototype
b.__proto__.__proto__ === Object.prototype
What is the prototype ?
prototype is an object automatically created as a special property of a function, which is used to establish the delegation (inheritance) chain, aka prototype chain.
When we create a function a, prototype is automatically created as a special property on a and saves the function code on as the constructor on prototype.
function Foo() {};
Foo.prototype // Object {constructor: function}
Foo.prototype.constructor === Foo // true
I'd love to consider this property as the place to store the properties (including methods) of a function object. That's also the reason why utility functions in JS are defined like Array.prototype.forEach() , Function.prototype.bind(), Object.prototype.toString().
Why to emphasize the property of a function?
{}.prototype // undefined;
(function(){}).prototype // Object {constructor: function}
// The example above shows object does not have the prototype property.
// But we have Object.prototype, which implies an interesting fact that
typeof Object === "function"
var obj = new Object();
So, Arary, Function, Objectare all functions. I should admit that this refreshes my impression on JS. I know functions are first-class citizen in JS but it seems that it is built on functions.
What's the difference between __proto__ and prototype?
__proto__a reference works on every object to refer to its [[Prototype]]property.
prototype is an object automatically created as a special property of a function, which is used to store the properties (including methods) of a function object.
With these two, we could mentally map out the prototype chain. Like this picture illustrates:
function Foo() {}
var b = new Foo();
b.__proto__ === Foo.prototype // true
Foo.__proto__ === Function.prototype // true
Function.prototype.__proto__ === Object.prototype // true

I know, I am late but let me try to simplify it.
Let us say there is a function
function Foo(message){
this.message = message ;
};
console.log(Foo.prototype);
Foo function will have a prototype object linked. So,Whenever we create a function in JavaScript, it always has a prototype object linked to it.
Now let us go ahead and create two objects using the function Foo.
var a = new Foo("a");
var b = new Foo("b");
console.log(a.message);
console.log(b.message);
Now we have two objects, object a and object b. Both are created
using constructor Foo. Keep in mind constructor is just a word here.
Object a and b both have a copy of message property.
These two objects a and b are linked to prototype object of constructor Foo.
On objects a and b, we can access Foo prototype using __proto__ property in all browsers and in IE we can use Object.getPrototypeOf(a) or Object.getPrototypeOf(b)
Now, Foo.prototype, a.__proto__, and b.__proto__ all denotes same object.
b.__proto__ === Object.getPrototypeOf(a);
a.__proto__ === Foo.prototype;
a.constructor.prototype === a.__proto__;
all of above would return true.
As we know, in JavaScript properties can be added dynamically. We can add property to object
Foo.prototype.Greet = function(){
console.log(this.message);
}
a.Greet();//a
b.Greet();//b
a.constructor.prototype.Greet();//undefined
As you see we added Greet() method in Foo.prototype but it is accessible in a and b or any other object which is constructed using Foo.
While executing a.Greet(), JavaScript will first search Greet in object a on property list. On not finding , it will go up in __proto__ chain of a. Since a.__proto__ and Foo.prototype is same object, JavaScript will find Greet() method and execute it.
I hope, now prototype and __proto__ is simplified a bit.

Another good way to understand it:
var foo = {}
/*
foo.constructor is Object, so foo.constructor.prototype is actually
Object.prototype; Object.prototype in return is what foo.__proto__ links to.
*/
console.log(foo.constructor.prototype === foo.__proto__);
// this proves what the above comment proclaims: Both statements evaluate to true.
console.log(foo.__proto__ === Object.prototype);
console.log(foo.constructor.prototype === Object.prototype);
Only after IE11 __proto__ is supported. Before that version, such as IE9, you could use the constructor to get the __proto__.

prototype
prototype is a property of a Function. It is the blueprint for creating objects by using that (constructor) function with new keyword.
__proto__
__proto__ is used in the lookup chain to resolve methods, properties. when an object is created (using constructor function with new keyword), __proto__ is set to (Constructor) Function.prototype
function Robot(name) {
this.name = name;
}
var robot = new Robot();
// the following are true
robot.__proto__ == Robot.prototype
robot.__proto__.__proto__ == Object.prototype
Here is my (imaginary) explanation to clear the confusion:
Imagine there is an imaginary class (blueprint/coockie cutter) associated with function. That imaginary class is used to instantiate objects. prototype is the extention mechanism (extention method in C#, or Swift Extension) to add things to that imaginary class.
function Robot(name) {
this.name = name;
}
The above can be imagined as:
// imaginary class
class Robot extends Object{
static prototype = Robot.class
// Robot.prototype is the way to add things to Robot class
// since Robot extends Object, therefore Robot.prototype.__proto__ == Object.prototype
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
}
So,
var robot = new Robot();
robot.__proto__ == Robot.prototype
robot.prototype == undefined
robot.__proto__.__proto__ == Object.prototype
Now adding method to the prototype of Robot:
Robot.prototype.move(x, y) = function(x, y){ Robot.position.x = x; Robot.position.y = y};
// Robot.prototype.move(x, y) ===(imagining)===> Robot.class.move(x, y)
The above can be imagined as extension of Robot class:
// Swift way of extention
extension Robot{
function move(x, y){
Robot.position.x = x; Robot.position.y = y
}
}
Which in turn,
// imaginary class
class Robot{
static prototype = Robot.class // Robot.prototype way to extend Robot class
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
// added by prototype (as like C# extension method)
function move(x, y){
Robot.position.x = x; Robot.position.y = y
};
}

I've made for myself a small drawing that represents the following code snippet:
var Cat = function() {}
var tom = new Cat()
I have a classical OO background, so it was helpful to represent the hierarchy in this manner. To help you read this diagram, treat the rectangles in the image as JavaScript objects. And yes, functions are also objects. ;)
Objects in JavaScript have properties and __proto__ is just one of them.
The idea behind this property is to point to the ancestor object in the (inheritance) hierarchy.
The root object in JavaScript is Object.prototype and all other objects are descendants of this one. The __proto__ property of the root object is null, which represents the end of inheritance chain.
You'll notice that prototype is a property of functions. Cat is a function, but also Function and Object are (native) functions. tom is not a function, thus it does not have this property.
The idea behind this property is to point to an object which will be used in the construction, i.e. when you call the new operator on that function.
Note that prototype objects (yellow rectangles) have another property called
constructor which points back to the respective function object. For
brevity reasons this was not depicted.
Indeed, when we create the tom object with new Cat(), the created object will have the __proto__ property set to the prototype object of the constructor function.
In the end, let us play with this diagram a bit. The following statements are true:
tom.__proto__ property points to the same object as Cat.prototype.
Cat.__proto__ points to the Function.prototype object, just like Function.__proto__ and Object.__proto__ do.
Cat.prototype.__proto__ and tom.__proto__.__proto__ point to the same object and that is Object.prototype.
Cheers!

[[Prototype]] :
[[Prototype]] is an internal hidden property of objects in JS and it is a reference to another object. Every object at the time of creation receives a non-null value for [[Prototype]]. Remember [[Get]] operation is invoked when we reference a property on an object like, myObject.a. If the object itself has a property, a on it then that property will be used.
let myObject= {
a: 2
};
console.log(myObject.a); // 2
But if the object itself directly does not have the requested property then [[Get]] operation will proceed to follow the [[Prototype]] link of the object. This process will continue until either a matching property name is found or the [[Prototype]] chain ends(at the built-in Object.prototype). If no matching property is found then undefined will be returned. Object.create(specifiedObject) creates an object with the [[Prototype]] linkage to the specified object.
let anotherObject= {
a: 2
};
// create an object linked to anotherObject
let myObject= Object.create(anotherObject);
console.log(myObject.a); // 2
Both for..in loop and in operator use [[Prototype]] chain lookup process. So if we use for..in loop to iterate over the properties of an object then all the enumerable properties which can be reached via that object's [[Prototype]] chain also will be enumerated along with the enumerable properties of the object itself. And when using in operator to test for the existence of a property on an object then in operator will check all the properties via [[Prototype]] linkage of the object regardless of their enumerability.
// for..in loop uses [[Prototype]] chain lookup process
let anotherObject= {
a: 2
};
let myObject= Object.create(anotherObject);
for(let k in myObject) {
console.log("found: " + k); // found: a
}
// in operator uses [[Prototype]] chain lookup process
console.log("a" in myObject); // true
.prototype :
.prototype is a property of functions in JS and it refers to an object having constructor property which stores all the properties(and methods) of the function object.
let foo= function(){}
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties
foo.id= "Walter White";
foo.job= "teacher";
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties and 2 more properties that we added to the fn object
/*
{constructor: f}
constructor: f()
id: "Walter White"
job: "teacher"
arguments: null
caller: null
length: 0
name: "foo"
prototype: {constructor: f}
__proto__: f()
[[FunctionLocation]]: VM789:1
[[Scopes]]: Scopes[2]
__proto__: Object
*/
But normal objects in JS does not have .prototype property. We know Object.prototype is the root object of all the objects in JS. So clearly Object is a function i.e. typeof Object === "function" . That means we also can create object from the Object function like, let myObj= new Object( ). Similarly Array, Function are also functions so we can use Array.prototype, Function.prototype to store all the generic properties of arrays and functions. So we can say JS is built on functions.
{}.prototype; // SyntaxError: Unexpected token '.'
(function(){}).prototype; // {constructor: f}
Also using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. In the below code, we have created an object, a from a fn, Letter and added 2 properties one to the fn object and another to the prototype object of the fn. Now if we try to access both of the properties on the newly created object, a then we only will be able to access the property added to the prototype object of the function. This is because the prototype object of the function is now on the [[Prototype]] chain of the newly created object, a.
let Letter= function(){}
let a= new Letter();
Letter.from= "Albuquerque";
Letter.prototype.to= "New Hampshire";
console.log(a.from); // undefined
console.log(a.to); // New Hampshire
.__proto__ :
.__proto__ is a property of objects in JS and it references the another object in the [[Prototype]] chain. We know [[Prototype]] is an internal hidden property of objects in JS and it references another object in the [[Prototype]] chain. We can get or set the object referred by the internal [[Prototype]] property in 2 ways
Object.getPrototypeOf(obj) / Object.setPrototypeOf(obj)
obj.__proto__
We can traverse the [[Prototype]] chain using: .__proto__.__proto__. . . Along with .constructor, .toString( ), .isPrototypeOf( ) our dunder proto property (__proto__) actually exists on the built-in Object.prototype root object, but available on any particular object. Our .__proto__ is actually a getter/setter. Implementation of .__proto__ in Object.prototype is as below :
Object.defineProperty(Object.prototype, "__proto__", {
get: function() {
return Object.getPrototypeOf(this);
},
set: function(o) {
Object.setPrototypeOf(this, o);
return o;
}
});
To retrieve the value of obj.__proto__ is like calling, obj.__proto__() which actually returns the calling of the getter fn, Object.getPrototypeOf(obj) which exists on Object.prototype object. Although .__proto__ is a settable property but we should not change [[Prototype]] of an already existing object because of performance issues.
Using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. Using .__proto__ property we can access the other object referenced by internal hidden [[Prototype]] property of the object. But __proto__ is not the same as [[Prototype]] rather a getter/setter for it. Consider below code :
let Letter= function() {}
let a= new Letter();
let b= new Letter();
let z= new Letter();
// output in console
a.__proto__ === Letter.prototype; // true
b.__proto__ === Letter.prototype; // true
z.__proto__ === Letter.prototype; // true
Letter.__proto__ === Function.prototype; // true
Function.prototype.__proto__ === Object.prototype; // true
Letter.prototype.__proto__ === Object.prototype; // true

To put it simply:
> var a = 1
undefined
> a.__proto__
[Number: 0]
> Number.prototype
[Number: 0]
> Number.prototype === a.__proto__
true
This allows you to attach properties to X.prototype AFTER objects of type X has been instantiated, and they will still get access to those new properties through the __proto__ reference which the Javascript-engine uses to walk up the prototype chain.

Prototype or Object.prototype is a property of an object literal. It represents the Object prototype object which you can override to add more properties or methods further along the prototype chain.
__proto__ is an accessor property (get and set function) that exposes the internal prototype of an object thru which it is accessed.
References:
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/prototype
http://www.w3schools.com/js/js_object_prototypes.asp
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/proto

Explanatory example:
function Dog(){}
Dog.prototype.bark = "woof"
let myPuppie = new Dog()
now, myPupppie has __proto__ property which points to Dog.prototype.
> myPuppie.__proto__
>> {bark: "woof", constructor: ƒ}
but myPuppie does NOT have a prototype property.
> myPuppie.prototype
>> undefined
So, __proto__ of mypuppie is the reference to the .prototype property of constructor function that was used to instantiate this object (and the current myPuppie object has "delegates to" relationship to this __proto__ object), while .prototype property of myPuppie is simply absent (since we did not set it).
Good explanation by MPJ here:
proto vs prototype - Object Creation in JavaScript

DEFINITIONS
(number inside the parenthesis () is a 'link' to the code that is written below)
prototype - an object that consists of:
=> functions (3) of this
particular ConstructorFunction.prototype(5) that are accessible by each
object (4) created or to-be-created through this constructor function (1)
=> the constructor function itself (1)
=> __proto__ of this particular object (prototype object)
__proto__ (dandor proto?) - a link BETWEEN any object (2) created through a particular constructor function (1), AND the prototype object's properties (5) of that constructor THAT allows each created object (2) to have access to the prototype's functions and methods (4) (__proto__ is by default included in every single object in JS)
CODE CLARIFICATION
1.
function Person (name, age) {
this.name = name;
this.age = age;
}
2.
var John = new Person(‘John’, 37);
// John is an object
3.
Person.prototype.getOlder = function() {
this.age++;
}
// getOlder is a key that has a value of the function
4.
John.getOlder();
5.
Person.prototype;

I'll try a 4th grade explanation:
Things are very simple. A prototype is an example of how something should be built. So:
I'm a function and I build new objects similar to my prototype
I'm an object and I was built using my __proto__ as an example
proof:
function Foo() { }
var bar = new Foo()
// `bar` is constructed from how Foo knows to construct objects
bar.__proto__ === Foo.prototype // => true
// bar is an instance - it does not know how to create objects
bar.prototype // => undefined

Every function you create has a property called prototype, and it starts off its life as an empty object. This property is of no use until you use this function as constructor function i.e. with the 'new' keyword.
This is often confused with the __proto__ property of an object. Some might get confused and except that the prototype property of an object might get them the proto of an object. But this is not case. prototype is used to get the __proto__ of an object created from a function constructor.
In the above example:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
console.log(eve.__proto__ == Person.prototype) // true
// this is exactly what prototype does, made Person.prototype equal to eve.__proto__
I hope it makes sense.

What about using __proto__ for static methods?
function Foo(name){
this.name = name
Foo.__proto__.collection.push(this)
Foo.__proto__.count++
}
Foo.__proto__.count=0
Foo.__proto__.collection=[]
var bar = new Foo('bar')
var baz = new Foo('baz')
Foo.count;//2
Foo.collection // [{...}, {...}]
bar.count // undefined

(function(){
let a = function(){console.log(this.b)};
a.prototype.b = 1;
a.__proto__.b = 2;
let q = new a();
console.log(a.b);
console.log(q.b)
})()
Try this code to understand

There is only one object that is used for protypal chaining. This object obviously has a name and a value: __proto__ is its name, and prototype is its value. That's all.
to make it even easier to grasp, look at the diagram on the top of this post (Diagram by dmitry soshnikov), you'll never find __proto__ points to something else other than prototype as its value.
The gist is this: __proto__ is the name that references the prototypal object, and prototype is the actual prototypal object.
It's like saying:
let x = {name: 'john'};
x is the object name (pointer), and {name: 'john'} is the actual object (data value).
NOTE: this just a massively simplified hint on how they are related on a high level.
Update: Here is a simple concrete javascript example for better illustration:
let x = new String("testing") // Or any other javascript object you want to create
Object.getPrototypeOf(x) === x.__proto__; // true
This means that when Object.getPrototypeOf(x) gets us the actual value of x (which is its prototype), is exactly what the __proto__ of x is pointing to. Therefore __proto__ is indeed pointing to the prototype of x. Thus __proto__ references x (pointer of x), and prototype is the value of x (its prototype).
I hope it's a bit clear now.

so many good answers exist for this question, but for recap and compact form of answer that have good details I add the following:
the first thing that we must consider is when JS was invented, computers have very low memory, so if we need a process for creating new object types, we must consider memory performance.
so they located methods that object created from that specific object type need, on the separate part of memory instead of every time we create a new object, store methods besides the object.
so if we reinvent the new operator and constructor function concept with JS's new features we have these steps:
and empty object. (that will be the final result of instantiation of object type)
let empty={}
we already know that for memory performance reasons all the methods that are needed for instances of an object type are located on the constructor function's prototype property. (functions are also objects so they can have properties)
so we reference the empty object's __protp__ to the location where those methods exist.
(we consider the function that we use conceptually as the constructor, named constructor.
empty.__proto__ = constructor.prototype
we must initialize object type values.
in JS function are disconnected from objects. with dot notation or methods like bind call apply that function objects have we must tell "what is the this context of the function".
let newFunc = constructor.bind(empty)
now we have a new function that has an empty object as this context.
after execution of this function. the empty object will be filled, and the result of instantiation of type object will be this empty object if defined constructor function doesn't return(as if that will be the result of the process)
so as you see __proto__ is a property of objects that refers to other objects(in JS functions are also object) prototype object property which consisted of properties that use across instances of a specific object type.
as you can guess from the phrase, functions are objects, functions also have __proto__ property so they can refer to other object's prototype properties. this is how prototype inheritance is implemented.

my understanding is: __proto__ and prototype are all served for the prototype chain technique . the difference is functions named with underscore(like __proto__) are not aim for developers invoked explicitly at all. in other words, they are just for some mechanisms like inherit etc. they are 'back-end'. but functions named without underscore are designed for invoked explicitly, they are 'front-end'.

__proto__ is the base to construct prototype and a constructor function eg: function human(){} has prototype which is shared via __proto__ in the new instance of the constructor function. A more detailed read here

As this rightly stated
__proto__ is the actual object that is used in the lookup chain to
resolve methods, etc. prototype is the object that is used to build
__proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype;
( new Foo ).prototype === undefined;
We can further note that __proto__ property of an object created using function constructor points towards the memory location pointed towards by prototype property of that respective constructor.
If we change the memory location of prototype of constructor function, __proto__ of derived object will still continue to point towards the original address space. Therefore to make common property available down the inheritance chain, always append property to constructor function prototype, instead of re-initializing it (which would change its memory address).
Consider the following example:
function Human(){
this.speed = 25;
}
var himansh = new Human();
Human.prototype.showSpeed = function(){
return this.speed;
}
himansh.__proto__ === Human.prototype; //true
himansh.showSpeed(); //25
//now re-initialzing the Human.prototype aka changing its memory location
Human.prototype = {lhs: 2, rhs:3}
//himansh.__proto__ will still continue to point towards the same original memory location.
himansh.__proto__ === Human.prototype; //false
himansh.showSpeed(); //25

what are the difference between __proto__ and prototype? [duplicate]

This figure again shows that every object has a prototype. Constructor
function Foo also has its own __proto__ which is Function.prototype,
and which in turn also references via its __proto__ property again to
the Object.prototype. Thus, repeat, Foo.prototype is just an explicit
property of Foo which refers to the prototype of b and c objects.
var b = new Foo(20);
var c = new Foo(30);
What are the differences between __proto__ and prototype?
The figure was taken from dmitrysoshnikov.com.
Note: there is now a 2nd edition (2017) to the above 2010 article.

__proto__ is the actual object that is used in the lookup chain to resolve methods, etc. prototype is the object that is used to build __proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype
( new Foo ).prototype === undefined

prototype is a property of a Function object. It is the prototype of objects constructed by that function.
__proto__ is an internal property of an object, pointing to its prototype. Current standards provide an equivalent Object.getPrototypeOf(obj) method, though the de facto standard __proto__ is quicker.
You can find instanceof relationships by comparing a function's prototype to an object's __proto__ chain, and you can break these relationships by changing prototype.
function Point(x, y) {
this.x = x;
this.y = y;
}
var myPoint = new Point();
// the following are all true
myPoint.__proto__ == Point.prototype
myPoint.__proto__.__proto__ == Object.prototype
myPoint instanceof Point;
myPoint instanceof Object;
Here Point is a constructor function, it builds an object (data structure) procedurally. myPoint is an object constructed by Point() so Point.prototype gets saved to myPoint.__proto__ at that time.

prototype property is created when a function is declared.
For instance:
function Person(dob){
this.dob = dob
};
Person.prototype property is created internally once you declare above function.
Many properties can be added to the Person.prototype which are shared by Person instances created using new Person().
// adds a new method age to the Person.prototype Object.
Person.prototype.age = function(){return date-dob};
It is worth noting that Person.prototype is an Object literal by default (it can be changed as required).
Every instance created using new Person() has a __proto__ property which points to the Person.prototype. This is the chain that is used to traverse to find a property of a particular object.
var person1 = new Person(somedate);
var person2 = new Person(somedate);
creates 2 instances of Person, these 2 objects can call age method of Person.prototype as person1.age, person2.age.
In the above picture from your question, you can see that Foo is a Function Object and therefore it has a __proto__ link to the Function.prototype which in turn is an instance of Object and has a __proto__ link to Object.prototype. The proto link ends here with __proto__ in the Object.prototype pointing to null.
Any object can have access to all the properties in its proto chain as linked by __proto__ , thus forming the basis for prototypal inheritance.
__proto__ is not a standard way of accessing the prototype chain, the standard but similar approach is to use Object.getPrototypeOf(obj).
Below code for instanceof operator gives a better understanding:
object instanceof Class operator returns true when an object is an instance of a Class, more specifically if Class.prototype is found in the proto chain of that object then the object is an instance of that Class.
function instanceOf(Func){
var obj = this;
while(obj !== null){
if(Object.getPrototypeOf(obj) === Func.prototype)
return true;
obj = Object.getPrototypeOf(obj);
}
return false;
}
The above method can be called as: instanceOf.call(object, Class) which return true if object is instance of Class.

To explain let us create a function
function a (name) {
this.name = name;
}
When JavaScript executes this code, it adds prototype property to a, prototype property is an object with two properties to it:
constructor
__proto__
So when we do
a.prototype it returns
constructor: a // function definition
__proto__: Object
Now as you can see constructor is nothing but the function a itself
and __proto__ points to the root level Object of JavaScript.
Let us see what happens when we use a function with new key word.
var b = new a ('JavaScript');
When JavaScript executes this code it does 4 things:
It creates a new object, an empty object // {}
It creates __proto__ on b and makes it point to a.prototype so b.__proto__ === a.prototype
It executes a.prototype.constructor (which is definition of function a ) with the newly created object (created in step#1) as its context (this), hence the name property passed as 'JavaScript' (which is added to this) gets added to newly created object.
It returns newly created object in (created in step#1) so var b gets assigned to newly created object.
Now if we add a.prototype.car = "BMW" and do
b.car, the output "BMW" appears.
this is because when JavaScript executed this code it searched for car property on b, it did not find then JavaScript used b.__proto__ (which was made to point to 'a.prototype' in step#2) and finds car property so return "BMW".

A nice way to think of it is...
prototype is used by constructor functions. It should've really been called something like, "prototypeToInstall", since that's what it is.
and __proto__ is that "installed prototype" on an object (that was created/installed upon the object from said constructor() function)

Prototype VS. __proto__ VS. [[Prototype]]
When creating a function, a property object called prototype is being created automatically (you didn't create it yourself) and is being attached to the function object (the constructor). Note: This new prototype object also points to, or has an internal-private link to, the native JavaScript Object.
Example:
function Foo () {
this.name = 'John Doe';
}
// Foo has an object property called prototype.
// prototype was created automatically when we declared the function Foo.
Foo.hasOwnProperty('prototype'); // true
// Now, we can assign properties and methods to it:
Foo.prototype.myName = function () {
return 'My name is ' + this.name;
}
If you create a new object out of Foo using the new keyword, you are basically creating (among other things) a new object that has an internal or private link to the function Foo's prototype we discussed earlier:
var b = new Foo();
b.[[Prototype]] === Foo.prototype // true
The private linkage to that function's object called double brackets prototype or just [[Prototype]]. Many browsers are providing us a public linkage to it that called __proto__!
To be more specific, __proto__ is actually a getter function that belong to the native JavaScript Object. It returns the internal-private prototype linkage of whatever the this binding is (returns the [[Prototype]] of b):
b.__proto__ === Foo.prototype // true
It is worth noting that starting of ECMAScript5, you can also use the getPrototypeOf method to get the internal private linkage:
Object.getPrototypeOf(b) === b.__proto__ // true
NOTE: this answer doesn't intend to cover the whole process of creating new objects or new constructors, but to help better understand what is __proto__, prototype and [[Prototype]] and how it works.

To make it a little bit clear in addition to above great answers:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
eve.__proto__ == Person.prototype //true
eve.prototype //undefined
Instances have __proto__, classes have prototype.

In JavaScript, a function can be used as a constructor. That means we can create objects out of them using the new keyword. Every constructor function comes with a built-in object chained with them. This built-in object is called a prototype. Instances of a constructor function use __proto__ to access the prototype property of its constructor function.
First we created a constructor: function Foo(){}. To be clear, Foo is just another function. But we can create an object from it with the new keyword. That's why we call it the constructor function
Every function has a unique property which is called the prototype property. So, Constructor function Foo has a prototype property which points to its prototype, which is Foo.prototype (see image).
Constructor functions are themselves a function which is an instance of a system constructor called the [[Function]] constructor. So we can say that function Foo is constructed by a [[Function]] constructor. So, __proto__ of our Foo function will point to the prototype of its constructor, which is Function.prototype.
Function.prototype is itself is nothing but an object which is constructed from another system constructor called [[Object]]. So, [[Object]] is the constructor of Function.prototype. So, we can say Function.prototype is an instance of [[Object]]. So __proto__ of Function.prototype points to Object.prototype.
Object.prototype is the last man standing in the prototype chain. I mean it has not been constructed. It's already there in the system. So its __proto__ points to null.
Now we come to instances of Foo. When we create an instance using new Foo(), it creates a new object which is an instance of Foo. That means Foo is the constructor of these instances. Here we created two instances (x and y). __proto__ of x and y thus points to Foo.prototype.

I think you need to know the difference between __proto__ , [[prototype]] and prototype.
The accepted answer is helpful, but it might imply (imperfectly) that __proto__ is something only relevant to objects created using new on a constructor function, which is not true.
To be more precise: __proto__ exists on EVERY object.
But what is __proto__ at all?
Well, it is an object referencing another object which is also a property of all objects, called [[prototype]].
It's worth mentioning that [[prototype]] is something that JavaScript handles internally and is inaccessible to the developer.
Why would we need a reference object to the property [[prototype]] (of all objects)?
Because JavaScript doesn't want to allow getting / setting the [[prototype]] directly, so it allows it through a middle layer which is __proto__. So you can think of __proto__ as a getter/setter of the [[prototype]] property.
What is prototype then?
It is something specific to functions(Initially defined in Function, i.e, Function.prototype and then prototypically inherited by newly created functions, and then again those functions give it to their children, forming a chain of prototypical inheritance).
JavaScript uses a parent function's prototype to set its child functions' [[prototype]] when that parent function is run with new (remember we said all objects have [[prototype]]? well, functions are objects too, so they have [[prototype]] as well). So when the [[prototype]] of a function(child) is set to the prototype of another function(parent), you will have this in the end:
let child = new Parent();
child.__proto__ === Parent.prototype // --> true.
(Remember child.[[prototype]] is inaccessible, so we checked it using __proto__.)
Notice 1: Whenever a property is not in the child, its __proto__ will be searched "implicitly". So for instance, if child.myprop returns a value, you can't say whether "myprop" was a property of the child, or of one of its parents' prototypes. This also means that you never need to do something like: child.__proto__.__proto__.myprop on your own, just child.myprop will do that for you automatically.
Notice 2: Even if the parent's prototype has items in it, the child's own prototype will be an empty object initially. You can add items to it or remove from it manually though, if you want to further extend the inhertance chain(add child[ren] to the child). Or it can be manipulated implicitly, e.g., using the class syntax.)
Notice 3: In case you need to set/get the [[prototype]] yourself, using __proto__ is a bit outdated and modern JavaScript suggests using Object.setPrototypeOf and Object.getPrototypeOf instead.

Summary:
The __proto__ property of an object is a property that maps to the prototype of the constructor function of the object. In other words:
instance.__proto__ === constructor.prototype // true
This is used to form the prototype chain of an object. The prototype chain is a lookup mechanism for properties on an object. If an object's property is accessed, JavaScript will first look on the object itself. If the property isn't found there, it will climb all the way up to protochain until it is found (or not)
Example:
function Person (name, city) {
this.name = name;
}
Person.prototype.age = 25;
const willem = new Person('Willem');
console.log(willem.__proto__ === Person.prototype); // the __proto__ property on the instance refers to the prototype of the constructor
console.log(willem.age); // 25 doesn't find it at willem object but is present at prototype
console.log(willem.__proto__.age); // now we are directly accessing the prototype of the Person function
Our first log results to true, this is because as mentioned the __proto__ property of the instance created by the constructor refers to the prototype property of the constructor. Remember, in JavaScript, functions are also Objects. Objects can have properties, and a default property of any function is one property named prototype.
Then, when this function is utilized as a constructor function, the object instantiated from it will receive a property called __proto__. And this __proto__ property refers to the prototype property of the constructor function (which by default every function has).
Why is this useful?
JavaScript has a mechanism when looking up properties on Objects which is called 'prototypal inheritance', here is what it basically does:
First, it's checked if the property is located on the Object itself. If so, this property is returned.
If the property is not located on the object itself, it will 'climb up the protochain'. It basically looks at the object referred to by the __proto__ property. There, it checks if the property is available on the object referred to by __proto__.
If the property isn't located on the __proto__ object, it will climb up the __proto__ chain, all the way up to Object object.
If it cannot find the property anywhere on the object and its prototype chain, it will return undefined.
For example:
function Person (name) {
this.name = name;
}
let mySelf = new Person('Willem');
console.log(mySelf.__proto__ === Person.prototype);
console.log(mySelf.__proto__.__proto__ === Object.prototype);

'use strict'
function A() {}
var a = new A();
class B extends A {}
var b = new B();
console.log('====='); // =====
console.log(B.__proto__ === A); // true
console.log(B.prototype.__proto__ === A.prototype); // true
console.log(b.__proto__ === B.prototype); // true
console.log(a.__proto__ === A.prototype); // true
console.log(A.__proto__ === Function.__proto__); // true
console.log(Object.__proto__ === Function.__proto__); // true
console.log(Object.prototype === Function.__proto__.__proto__); // true
console.log(Object.prototype.__proto__ === null); // true
In JavaScript, Every object(function is object too!) has a __proto__ property, the property is reference to its prototype.
When we use the new operator with a constructor to create a new object,
the new object's __proto__ property will be set with constructor's prototype property,
then the constructor will be call by the new object,
in that process "this" will be a reference to the new object in the constructor scope, finally return the new object.
Constructor's prototype is __proto__ property, Constructor's prototype property is work with the new operator.
Constructor must be a function, but function not always is constructor even if it has prototype property.
Prototype chain actually is object's __proto__ property to reference its prototype,
and the prototype's __proto__ property to reference the prototype's prototype, and so on,
until to reference Object's prototype's __proto__ property which is reference to null.
For example:
console.log(a.constructor === A); // true
// "a" don't have constructor,
// so it reference to A.prototype by its ``__proto__`` property,
// and found constructor is reference to A
[[Prototype]] and __proto__ property actually is same thing.
We can use Object's getPrototypeOf method to get something's prototype.
console.log(Object.getPrototypeOf(a) === a.__proto__); // true
Any function we written can be use to create an object with the new operator,
so anyone of those functions can be a constructor.

I happen to be learning prototype from You Don't Know JS: this & Object Prototypes, which is a wonderful book to understand the design underneath and clarify so many misconceptions (that's why I'm trying to avoid using inheritance and things like instanceof).
But I have the same question as people asked here. Several answers are really helpful and enlightening. I'd also love to share my understandings.
What is a prototype?
Objects in JavaScript have an internal property, denoted in the specification as[[Prototype]], which is simply a reference to another object. Almost all objects are given a non-nullvalue for this property, at the time of their creation.
How to get an object's prototype?
via __proto__or Object.getPrototypeOf
var a = { name: "wendi" };
a.__proto__ === Object.prototype // true
Object.getPrototypeOf(a) === Object.prototype // true
function Foo() {};
var b = new Foo();
b.__proto__ === Foo.prototype
b.__proto__.__proto__ === Object.prototype
What is the prototype ?
prototype is an object automatically created as a special property of a function, which is used to establish the delegation (inheritance) chain, aka prototype chain.
When we create a function a, prototype is automatically created as a special property on a and saves the function code on as the constructor on prototype.
function Foo() {};
Foo.prototype // Object {constructor: function}
Foo.prototype.constructor === Foo // true
I'd love to consider this property as the place to store the properties (including methods) of a function object. That's also the reason why utility functions in JS are defined like Array.prototype.forEach() , Function.prototype.bind(), Object.prototype.toString().
Why to emphasize the property of a function?
{}.prototype // undefined;
(function(){}).prototype // Object {constructor: function}
// The example above shows object does not have the prototype property.
// But we have Object.prototype, which implies an interesting fact that
typeof Object === "function"
var obj = new Object();
So, Arary, Function, Objectare all functions. I should admit that this refreshes my impression on JS. I know functions are first-class citizen in JS but it seems that it is built on functions.
What's the difference between __proto__ and prototype?
__proto__a reference works on every object to refer to its [[Prototype]]property.
prototype is an object automatically created as a special property of a function, which is used to store the properties (including methods) of a function object.
With these two, we could mentally map out the prototype chain. Like this picture illustrates:
function Foo() {}
var b = new Foo();
b.__proto__ === Foo.prototype // true
Foo.__proto__ === Function.prototype // true
Function.prototype.__proto__ === Object.prototype // true

I know, I am late but let me try to simplify it.
Let us say there is a function
function Foo(message){
this.message = message ;
};
console.log(Foo.prototype);
Foo function will have a prototype object linked. So,Whenever we create a function in JavaScript, it always has a prototype object linked to it.
Now let us go ahead and create two objects using the function Foo.
var a = new Foo("a");
var b = new Foo("b");
console.log(a.message);
console.log(b.message);
Now we have two objects, object a and object b. Both are created
using constructor Foo. Keep in mind constructor is just a word here.
Object a and b both have a copy of message property.
These two objects a and b are linked to prototype object of constructor Foo.
On objects a and b, we can access Foo prototype using __proto__ property in all browsers and in IE we can use Object.getPrototypeOf(a) or Object.getPrototypeOf(b)
Now, Foo.prototype, a.__proto__, and b.__proto__ all denotes same object.
b.__proto__ === Object.getPrototypeOf(a);
a.__proto__ === Foo.prototype;
a.constructor.prototype === a.__proto__;
all of above would return true.
As we know, in JavaScript properties can be added dynamically. We can add property to object
Foo.prototype.Greet = function(){
console.log(this.message);
}
a.Greet();//a
b.Greet();//b
a.constructor.prototype.Greet();//undefined
As you see we added Greet() method in Foo.prototype but it is accessible in a and b or any other object which is constructed using Foo.
While executing a.Greet(), JavaScript will first search Greet in object a on property list. On not finding , it will go up in __proto__ chain of a. Since a.__proto__ and Foo.prototype is same object, JavaScript will find Greet() method and execute it.
I hope, now prototype and __proto__ is simplified a bit.

Another good way to understand it:
var foo = {}
/*
foo.constructor is Object, so foo.constructor.prototype is actually
Object.prototype; Object.prototype in return is what foo.__proto__ links to.
*/
console.log(foo.constructor.prototype === foo.__proto__);
// this proves what the above comment proclaims: Both statements evaluate to true.
console.log(foo.__proto__ === Object.prototype);
console.log(foo.constructor.prototype === Object.prototype);
Only after IE11 __proto__ is supported. Before that version, such as IE9, you could use the constructor to get the __proto__.

prototype
prototype is a property of a Function. It is the blueprint for creating objects by using that (constructor) function with new keyword.
__proto__
__proto__ is used in the lookup chain to resolve methods, properties. when an object is created (using constructor function with new keyword), __proto__ is set to (Constructor) Function.prototype
function Robot(name) {
this.name = name;
}
var robot = new Robot();
// the following are true
robot.__proto__ == Robot.prototype
robot.__proto__.__proto__ == Object.prototype
Here is my (imaginary) explanation to clear the confusion:
Imagine there is an imaginary class (blueprint/coockie cutter) associated with function. That imaginary class is used to instantiate objects. prototype is the extention mechanism (extention method in C#, or Swift Extension) to add things to that imaginary class.
function Robot(name) {
this.name = name;
}
The above can be imagined as:
// imaginary class
class Robot extends Object{
static prototype = Robot.class
// Robot.prototype is the way to add things to Robot class
// since Robot extends Object, therefore Robot.prototype.__proto__ == Object.prototype
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
}
So,
var robot = new Robot();
robot.__proto__ == Robot.prototype
robot.prototype == undefined
robot.__proto__.__proto__ == Object.prototype
Now adding method to the prototype of Robot:
Robot.prototype.move(x, y) = function(x, y){ Robot.position.x = x; Robot.position.y = y};
// Robot.prototype.move(x, y) ===(imagining)===> Robot.class.move(x, y)
The above can be imagined as extension of Robot class:
// Swift way of extention
extension Robot{
function move(x, y){
Robot.position.x = x; Robot.position.y = y
}
}
Which in turn,
// imaginary class
class Robot{
static prototype = Robot.class // Robot.prototype way to extend Robot class
var __proto__;
var name = "";
// constructor
function Robot(name) {
this.__proto__ = prototype;
prototype = undefined;
this.name = name;
}
// added by prototype (as like C# extension method)
function move(x, y){
Robot.position.x = x; Robot.position.y = y
};
}

I've made for myself a small drawing that represents the following code snippet:
var Cat = function() {}
var tom = new Cat()
I have a classical OO background, so it was helpful to represent the hierarchy in this manner. To help you read this diagram, treat the rectangles in the image as JavaScript objects. And yes, functions are also objects. ;)
Objects in JavaScript have properties and __proto__ is just one of them.
The idea behind this property is to point to the ancestor object in the (inheritance) hierarchy.
The root object in JavaScript is Object.prototype and all other objects are descendants of this one. The __proto__ property of the root object is null, which represents the end of inheritance chain.
You'll notice that prototype is a property of functions. Cat is a function, but also Function and Object are (native) functions. tom is not a function, thus it does not have this property.
The idea behind this property is to point to an object which will be used in the construction, i.e. when you call the new operator on that function.
Note that prototype objects (yellow rectangles) have another property called
constructor which points back to the respective function object. For
brevity reasons this was not depicted.
Indeed, when we create the tom object with new Cat(), the created object will have the __proto__ property set to the prototype object of the constructor function.
In the end, let us play with this diagram a bit. The following statements are true:
tom.__proto__ property points to the same object as Cat.prototype.
Cat.__proto__ points to the Function.prototype object, just like Function.__proto__ and Object.__proto__ do.
Cat.prototype.__proto__ and tom.__proto__.__proto__ point to the same object and that is Object.prototype.
Cheers!

[[Prototype]] :
[[Prototype]] is an internal hidden property of objects in JS and it is a reference to another object. Every object at the time of creation receives a non-null value for [[Prototype]]. Remember [[Get]] operation is invoked when we reference a property on an object like, myObject.a. If the object itself has a property, a on it then that property will be used.
let myObject= {
a: 2
};
console.log(myObject.a); // 2
But if the object itself directly does not have the requested property then [[Get]] operation will proceed to follow the [[Prototype]] link of the object. This process will continue until either a matching property name is found or the [[Prototype]] chain ends(at the built-in Object.prototype). If no matching property is found then undefined will be returned. Object.create(specifiedObject) creates an object with the [[Prototype]] linkage to the specified object.
let anotherObject= {
a: 2
};
// create an object linked to anotherObject
let myObject= Object.create(anotherObject);
console.log(myObject.a); // 2
Both for..in loop and in operator use [[Prototype]] chain lookup process. So if we use for..in loop to iterate over the properties of an object then all the enumerable properties which can be reached via that object's [[Prototype]] chain also will be enumerated along with the enumerable properties of the object itself. And when using in operator to test for the existence of a property on an object then in operator will check all the properties via [[Prototype]] linkage of the object regardless of their enumerability.
// for..in loop uses [[Prototype]] chain lookup process
let anotherObject= {
a: 2
};
let myObject= Object.create(anotherObject);
for(let k in myObject) {
console.log("found: " + k); // found: a
}
// in operator uses [[Prototype]] chain lookup process
console.log("a" in myObject); // true
.prototype :
.prototype is a property of functions in JS and it refers to an object having constructor property which stores all the properties(and methods) of the function object.
let foo= function(){}
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties
foo.id= "Walter White";
foo.job= "teacher";
console.log(foo.prototype);
// returns {constructor: f} object which now contains all the default properties and 2 more properties that we added to the fn object
/*
{constructor: f}
constructor: f()
id: "Walter White"
job: "teacher"
arguments: null
caller: null
length: 0
name: "foo"
prototype: {constructor: f}
__proto__: f()
[[FunctionLocation]]: VM789:1
[[Scopes]]: Scopes[2]
__proto__: Object
*/
But normal objects in JS does not have .prototype property. We know Object.prototype is the root object of all the objects in JS. So clearly Object is a function i.e. typeof Object === "function" . That means we also can create object from the Object function like, let myObj= new Object( ). Similarly Array, Function are also functions so we can use Array.prototype, Function.prototype to store all the generic properties of arrays and functions. So we can say JS is built on functions.
{}.prototype; // SyntaxError: Unexpected token '.'
(function(){}).prototype; // {constructor: f}
Also using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. In the below code, we have created an object, a from a fn, Letter and added 2 properties one to the fn object and another to the prototype object of the fn. Now if we try to access both of the properties on the newly created object, a then we only will be able to access the property added to the prototype object of the function. This is because the prototype object of the function is now on the [[Prototype]] chain of the newly created object, a.
let Letter= function(){}
let a= new Letter();
Letter.from= "Albuquerque";
Letter.prototype.to= "New Hampshire";
console.log(a.from); // undefined
console.log(a.to); // New Hampshire
.__proto__ :
.__proto__ is a property of objects in JS and it references the another object in the [[Prototype]] chain. We know [[Prototype]] is an internal hidden property of objects in JS and it references another object in the [[Prototype]] chain. We can get or set the object referred by the internal [[Prototype]] property in 2 ways
Object.getPrototypeOf(obj) / Object.setPrototypeOf(obj)
obj.__proto__
We can traverse the [[Prototype]] chain using: .__proto__.__proto__. . . Along with .constructor, .toString( ), .isPrototypeOf( ) our dunder proto property (__proto__) actually exists on the built-in Object.prototype root object, but available on any particular object. Our .__proto__ is actually a getter/setter. Implementation of .__proto__ in Object.prototype is as below :
Object.defineProperty(Object.prototype, "__proto__", {
get: function() {
return Object.getPrototypeOf(this);
},
set: function(o) {
Object.setPrototypeOf(this, o);
return o;
}
});
To retrieve the value of obj.__proto__ is like calling, obj.__proto__() which actually returns the calling of the getter fn, Object.getPrototypeOf(obj) which exists on Object.prototype object. Although .__proto__ is a settable property but we should not change [[Prototype]] of an already existing object because of performance issues.
Using new operator if we create objects from a function then internal hidden [[Prototype]] property of those newly created objects will point to the object referenced by the .prototype property of the original function. Using .__proto__ property we can access the other object referenced by internal hidden [[Prototype]] property of the object. But __proto__ is not the same as [[Prototype]] rather a getter/setter for it. Consider below code :
let Letter= function() {}
let a= new Letter();
let b= new Letter();
let z= new Letter();
// output in console
a.__proto__ === Letter.prototype; // true
b.__proto__ === Letter.prototype; // true
z.__proto__ === Letter.prototype; // true
Letter.__proto__ === Function.prototype; // true
Function.prototype.__proto__ === Object.prototype; // true
Letter.prototype.__proto__ === Object.prototype; // true

To put it simply:
> var a = 1
undefined
> a.__proto__
[Number: 0]
> Number.prototype
[Number: 0]
> Number.prototype === a.__proto__
true
This allows you to attach properties to X.prototype AFTER objects of type X has been instantiated, and they will still get access to those new properties through the __proto__ reference which the Javascript-engine uses to walk up the prototype chain.

Prototype or Object.prototype is a property of an object literal. It represents the Object prototype object which you can override to add more properties or methods further along the prototype chain.
__proto__ is an accessor property (get and set function) that exposes the internal prototype of an object thru which it is accessed.
References:
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/prototype
http://www.w3schools.com/js/js_object_prototypes.asp
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/proto

Explanatory example:
function Dog(){}
Dog.prototype.bark = "woof"
let myPuppie = new Dog()
now, myPupppie has __proto__ property which points to Dog.prototype.
> myPuppie.__proto__
>> {bark: "woof", constructor: ƒ}
but myPuppie does NOT have a prototype property.
> myPuppie.prototype
>> undefined
So, __proto__ of mypuppie is the reference to the .prototype property of constructor function that was used to instantiate this object (and the current myPuppie object has "delegates to" relationship to this __proto__ object), while .prototype property of myPuppie is simply absent (since we did not set it).
Good explanation by MPJ here:
proto vs prototype - Object Creation in JavaScript

DEFINITIONS
(number inside the parenthesis () is a 'link' to the code that is written below)
prototype - an object that consists of:
=> functions (3) of this
particular ConstructorFunction.prototype(5) that are accessible by each
object (4) created or to-be-created through this constructor function (1)
=> the constructor function itself (1)
=> __proto__ of this particular object (prototype object)
__proto__ (dandor proto?) - a link BETWEEN any object (2) created through a particular constructor function (1), AND the prototype object's properties (5) of that constructor THAT allows each created object (2) to have access to the prototype's functions and methods (4) (__proto__ is by default included in every single object in JS)
CODE CLARIFICATION
1.
function Person (name, age) {
this.name = name;
this.age = age;
}
2.
var John = new Person(‘John’, 37);
// John is an object
3.
Person.prototype.getOlder = function() {
this.age++;
}
// getOlder is a key that has a value of the function
4.
John.getOlder();
5.
Person.prototype;

I'll try a 4th grade explanation:
Things are very simple. A prototype is an example of how something should be built. So:
I'm a function and I build new objects similar to my prototype
I'm an object and I was built using my __proto__ as an example
proof:
function Foo() { }
var bar = new Foo()
// `bar` is constructed from how Foo knows to construct objects
bar.__proto__ === Foo.prototype // => true
// bar is an instance - it does not know how to create objects
bar.prototype // => undefined

Every function you create has a property called prototype, and it starts off its life as an empty object. This property is of no use until you use this function as constructor function i.e. with the 'new' keyword.
This is often confused with the __proto__ property of an object. Some might get confused and except that the prototype property of an object might get them the proto of an object. But this is not case. prototype is used to get the __proto__ of an object created from a function constructor.
In the above example:
function Person(name){
this.name = name
};
var eve = new Person("Eve");
console.log(eve.__proto__ == Person.prototype) // true
// this is exactly what prototype does, made Person.prototype equal to eve.__proto__
I hope it makes sense.

What about using __proto__ for static methods?
function Foo(name){
this.name = name
Foo.__proto__.collection.push(this)
Foo.__proto__.count++
}
Foo.__proto__.count=0
Foo.__proto__.collection=[]
var bar = new Foo('bar')
var baz = new Foo('baz')
Foo.count;//2
Foo.collection // [{...}, {...}]
bar.count // undefined

(function(){
let a = function(){console.log(this.b)};
a.prototype.b = 1;
a.__proto__.b = 2;
let q = new a();
console.log(a.b);
console.log(q.b)
})()
Try this code to understand

There is only one object that is used for protypal chaining. This object obviously has a name and a value: __proto__ is its name, and prototype is its value. That's all.
to make it even easier to grasp, look at the diagram on the top of this post (Diagram by dmitry soshnikov), you'll never find __proto__ points to something else other than prototype as its value.
The gist is this: __proto__ is the name that references the prototypal object, and prototype is the actual prototypal object.
It's like saying:
let x = {name: 'john'};
x is the object name (pointer), and {name: 'john'} is the actual object (data value).
NOTE: this just a massively simplified hint on how they are related on a high level.
Update: Here is a simple concrete javascript example for better illustration:
let x = new String("testing") // Or any other javascript object you want to create
Object.getPrototypeOf(x) === x.__proto__; // true
This means that when Object.getPrototypeOf(x) gets us the actual value of x (which is its prototype), is exactly what the __proto__ of x is pointing to. Therefore __proto__ is indeed pointing to the prototype of x. Thus __proto__ references x (pointer of x), and prototype is the value of x (its prototype).
I hope it's a bit clear now.

so many good answers exist for this question, but for recap and compact form of answer that have good details I add the following:
the first thing that we must consider is when JS was invented, computers have very low memory, so if we need a process for creating new object types, we must consider memory performance.
so they located methods that object created from that specific object type need, on the separate part of memory instead of every time we create a new object, store methods besides the object.
so if we reinvent the new operator and constructor function concept with JS's new features we have these steps:
and empty object. (that will be the final result of instantiation of object type)
let empty={}
we already know that for memory performance reasons all the methods that are needed for instances of an object type are located on the constructor function's prototype property. (functions are also objects so they can have properties)
so we reference the empty object's __protp__ to the location where those methods exist.
(we consider the function that we use conceptually as the constructor, named constructor.
empty.__proto__ = constructor.prototype
we must initialize object type values.
in JS function are disconnected from objects. with dot notation or methods like bind call apply that function objects have we must tell "what is the this context of the function".
let newFunc = constructor.bind(empty)
now we have a new function that has an empty object as this context.
after execution of this function. the empty object will be filled, and the result of instantiation of type object will be this empty object if defined constructor function doesn't return(as if that will be the result of the process)
so as you see __proto__ is a property of objects that refers to other objects(in JS functions are also object) prototype object property which consisted of properties that use across instances of a specific object type.
as you can guess from the phrase, functions are objects, functions also have __proto__ property so they can refer to other object's prototype properties. this is how prototype inheritance is implemented.

my understanding is: __proto__ and prototype are all served for the prototype chain technique . the difference is functions named with underscore(like __proto__) are not aim for developers invoked explicitly at all. in other words, they are just for some mechanisms like inherit etc. they are 'back-end'. but functions named without underscore are designed for invoked explicitly, they are 'front-end'.

__proto__ is the base to construct prototype and a constructor function eg: function human(){} has prototype which is shared via __proto__ in the new instance of the constructor function. A more detailed read here

As this rightly stated
__proto__ is the actual object that is used in the lookup chain to
resolve methods, etc. prototype is the object that is used to build
__proto__ when you create an object with new:
( new Foo ).__proto__ === Foo.prototype;
( new Foo ).prototype === undefined;
We can further note that __proto__ property of an object created using function constructor points towards the memory location pointed towards by prototype property of that respective constructor.
If we change the memory location of prototype of constructor function, __proto__ of derived object will still continue to point towards the original address space. Therefore to make common property available down the inheritance chain, always append property to constructor function prototype, instead of re-initializing it (which would change its memory address).
Consider the following example:
function Human(){
this.speed = 25;
}
var himansh = new Human();
Human.prototype.showSpeed = function(){
return this.speed;
}
himansh.__proto__ === Human.prototype; //true
himansh.showSpeed(); //25
//now re-initialzing the Human.prototype aka changing its memory location
Human.prototype = {lhs: 2, rhs:3}
//himansh.__proto__ will still continue to point towards the same original memory location.
himansh.__proto__ === Human.prototype; //false
himansh.showSpeed(); //25

Best way to retrieve the prototype of a JS object

Trying to understand Prototypes in Javascript. For this example:
var obj = new Function();
obj.prototype.x = "a";
Why do I get different results from
console.log(obj.__proto__);
and
console.log(obj.prototype);
Thanks

In:
> var obj = new Function();
a new function object is created whose internal [[Prototype]] (or __proto__ in browsers that support it) references Function.prototype, i.e. the built–in Function constructor's public prototype and assigned to the variable obj.
Because obj is a Function object, it has a prototype property by default just in case it is to be used as a constructor.
In:
> obj.prototype.x = "a";
a new x property is added to obj.prototype that is assigned a value of the string 'a'. Note that obj only has a prototype property by default because it's a Function object.
So:
obj.prototype === obj.__proto__
is essentially:
obj.prototype === Function.prototype
which is clearly false.
So to answer the question "Best way to retrieve the prototype of a JS object" then you can access a constructor's public prototype through its prototype property.
You can access a instance's internal [[Prototype]] using ES5 Object.getPrototypeOf, however it may not be supported everywhere.
You can also access a instance's internal [[Prototype]] using the non–standard __proto__ where supported.
A more general solution is to keep a reference to the constructor's prototype at the time the instance is created (since changing the constructor's prototype at some later stage will not change the [[Prototype]] of instances that have already been created).
So in a general case you might do:
function Foo() {
this.internalProto = Foo.prototype;
}
var foo = new Foo();
// ES5, where supported
Object.getPrototypeof(foo) == Foo.prototype; // true
foo.internalProto == Foo.prototype; // true
// Non–standard, Where supported
foo.internalProto == foo.__proto__; // true

According to this source: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/prototype
Object.prototype.__proto__ points to the object which was used as
prototype when the object was instantiated.
It simply means that object used as prototype to create Function object was empty function, and that's why you have function Empty() {} in the output. You can observe it here:
console.log(Function.prototype);
var func = new Function();
console.log(func.__proto__);
console.log(func.prototype);
// OUTPUT:
// function Empty() {}
// function Empty() {}
// Object {}
__proto__ of an empty object (e.g. var a = {}) is Object {} because this is, what was used to create base of your object (in other words Object.prototype was used). And prototype is not even available as a property of a, because you've created a totally empty object, so there's nothing.
Also notice that __proto__ is now deprecated.
Why? I don't know, but I have never used it so I don't care :)
prototype is a different thing, e.g.
Changes to the Object prototype object are propagated to all objects
unless the properties and methods subject to those changes are
overridden further along the prototype chain.
This is why you need prototype and you don't care about __proto__ in real life. If I'm wrong please show me useful usage of __proto__.
Hope it's clearer now. And to answer your original question:
Prototype of a JS object can be retrieved only by using prototype property, as __proto__ contains sth different. If prototype property doesn't exist, there is no prototype of the JS object, even if sth was used in the process of instantiation.

Accordint to the MDN, obj.__proto__ has not been standardized.
So while obj.prototype has a clear standardized behav8our accross browsers, obj.__proto__ behaves differently in different browsers.

You're looking at this sideways...
.prototype and .__proto__ are the same object (or are at one specific point in time)...
BUUUUUT they're propertes of different objects.
var Human = function (name) {
this.num_eyes = 2;
this.num_heads = 1;
this.name = name;
};
Human.prototype.die = function () { this.isAlive = false; };
var herman = new Human("Herman");
herman.__proto__.die === Human.prototype.die; // true
.__proto__ is a link to the CONSTRUCTOR .prototype (and typically, is the SAME object)
It's almost like this:
var Human = function () {
this = {};
this.num_eyes = 2;
// ......
this.__proto__ = Human.prototype;
};
That isn't exactly how constructors work, but really, that's the idea.
And that's why .__proto__ and .prototype aren't the same thing.
Because you're looking in the wrong place.
So if:
var herman = new Human();
herman.__proto__ === Human.prototype;
var Human = new Function ();
...so logic then states that Human.__proto__ === Function.prototype;
...and if Human and Function aren't the same object, then their .prototype properties aren't going to be the same (unless you overwrite one with the other Human.prototype = Function.prototype; Human.__proto__ === Human.prototype; //true

It is said that all Javascript objects have a prototype property, but I only see foo.prototype if foo is a function?

It is often said that every Javascript object has a prototype property, but I find that foo.prototype has a value only if foo is a function.
On Chrome and Firefox, obj.__proto__ has a value -- is this the said prototype property? But on IE 9, it won't work (is there some way that can?), and I thought by prototype property, that means obj.prototype should work?
I understand that Object.getPrototypeOf(obj) seems to show this prototype property, but why need a special method to get it? Why not just like person.name, which is to get the name property of the person object?
Update: by the way, obj.constructor.prototype seems to sometimes be that prototype, but sometimes not, as in the following code done with Prototypal inheritance with no constructor: (this method is in the Pro Javascript Design Patterns book by Harmes and Diaz by Apress 2008, p. 46)
var Person = {
name: 'default value',
getName: function() {
return this.name;
}
}
var reader = clone(Person);
console.log(reader.getName());
reader.name = "Ang Lee";
console.log(reader.getName());
function clone(obj) {
function F() {};
F.prototype = obj;
return new F;
}
console.log("the prototype of reader is", Object.getPrototypeOf(reader));
console.log(Object.getPrototypeOf(reader) === reader.constructor.prototype);
console.log(Object.getPrototypeOf(reader) == reader.constructor.prototype);
console.log(Object.getPrototypeOf(reader) === reader.__proto__);
console.log(Object.getPrototypeOf(reader) == reader.__proto__);
the result will show false, false, true, true for the last 4 lines.

Every JavaScript object has an internal "prototype" property, often called [[prototype]], which points to the object from which it directly inherits. This is exposed in FF and Chrome by the non-standard __proto__ property. Object.getPrototypeOf is a getter for this internal property.
Every JavaScript function [object] has a property prototype, which is initialized with an [nearly] empty object. When you create a new instance of this function by calling it as a constructor, the [[prototype]] of that new object will point to the constructor's prototype object.
If you get the [[prototype]] of a function (every function is an object, so it has one), it will result in the Function.prototype object from which functions inherit their methods (like bind, call, apply etc). See also Why functions prototype is chained repeatedly? on that.

It is the constructor of every Object that has a prototype. So for some foo, baror foobar:
var foo = {};
console.log(foo.constructor.prototype); //=> Object
var bar = 5;
console.log(bar.constructor.prototype); //=> Number
function Foobar(){}
var foobar = new Foobar; //Foobar used a constructor
console.log(foobar.constructor.prototype); //=> Foobar