Merkle Trees

A Merkle tree is a cryptographic data structure designed by Ralph Merkle in the late 1970s and has grown dramatically in prominence in the last few years, inasmuch as variants of Merkle trees are at the core of most blockchain systems.

A Merkle tree makes use of cryptographic hashes to enable efficient cryptographic proofs of the authenticity of data stored in the tree. In particular, for a Merkle tree containing \(2^n\) data items, it only takes \(n\) hash computations to prove that a particular item is in the tree.

In this section, we build a very simple, but canonical, Merkle tree and prove it correct and cryptographically secure. And we’ll use several indexed inductive types to do it. Thanks to Aseem Rastogi for this example!


Merkle trees have many applications. To motivate our presentation here, consider the following simple scenario.

A content provider (someone like, say, the New York Times) has a large archive of digital artifacts—documents, multimedia files, etc. These artifacts are circulated among users, but when receiving an artifact one may question its authenticity. One way to ensure the authenticity of received artifacts is for the content provider to use a digital signature based on a public-key cryptosystem and for users to verify these signatures upon receiving an artifact. However, signatures can be quite heavyweight for certain applications.

Instead, the content provider can organize their archive into a Merkle tree, a tree of hashes with the artifacts themselves stored at the leaves, such that a single hash associated with the root node of the tree authenticates all the artifacts in the tree. By publishing just this root hash, and associating with each artifact a path in the tree from the root to it, a skeptical client can quickly check using a small number of hash computations (logarithmic in the size of the entire archive) whether or not a given artifact is authentic (by recomputing the root hash and checking if it matches the known published root hash).


Our Merkle tree will be a full binary tree of height \(n\) storing \(2^n\) data items and their corresponding hashes at the nodes. The main idea of a Merkle tree is for each internal node to also maintain a hash of the hashes stored at each of its children. If the hash algorithm being used is cryptographically secure, in the sense that it is collision resistant (i.e., it is computationally hard to find two strings that hash to the same value), then the hash associated with the root node authenticates the content of the entire tree.

Informally, a Merkle tree is an authenticated data structure in that it is computationally hard to tamper with any of the data items in the tree while still producing the same root hash. Further, to prove that a particular data item d is in the tree, it suffices to provide the hashes associated with the nodes in the path from the root to that the leaf containing that item d, and one can easily check by comparing hashes that the claimed path is accurate. In fact, we can prove that if a claimed path through the tree attests to the presence of some other item d' <> d, then we can construct a collision on the underlying hash algorithm—this property wil be our main proof of security.


We’ll model the resources and the hashes we store in our tree as strings of characters. F* standard library FStar.String provides some utilities to work with strings.

In the code listing below, we define the following

  • lstring n, the type of strings of length n. Like the vec type, lstring is a length-indexed type; unlike vector it is defined using a refinement type rather than an indexed inductive type. Defining indexed types using refinements is quite common in F*.

  • concat, a utility to concatenate strings, with its type proving that the resulting string’s length is the sum of the lengths of the input strings.

  • hash_size and hash, a parameter of our development describing the length in characters of a hash function. The F* keyword assume allows you to assume the existence of a symbol at a given type. Use it with care, since you can trivially prove anything by including an assume nonsense : False.

  • The type of resources we store in the tree will just be resource, an alias for string.

//Length-indexed strings
let lstring (n:nat) = s:string{String.length s == n}

//Concatenating strings sums their lengths
let concat #n #m (s0:lstring n) (s1:lstring m)
  : lstring (m + n)
  = FStar.String.concat_length s0 s1;
    s0 ^ s1

//A parameter, lenght of the hash in characters, 
//e.g., this would be 32, if a character is 1 byte
//and we're using SHA-256
val hash_size:nat

//The type of a hashed value
let hash_t = lstring hash_size

//The hash function itself
val hash (m:string) : hash_t

//The type of resources stored in the tree
let resource = string

Defining the Merkle tree

The inductive type mtree below defines our Merkle tree. The type has two indices, such that mtree n h is the type of a Merkle tree of height n whose root node is associated with the hash h.

Leaves are trees of height 0 and are constructed using L res, where the hash associated with this node is just hash res, the hash of the resource stored at the leaf.

Internal nodes of the tree are constructed using N left right, where both the left and right trees have the same height n, producing a tree of height n + 1. More interestingly, the hash associated with N left right is hash (concat hl hr), the hash of the concatenation of hashes of the left and right subtrees.

type mtree: nat -> hash_t -> Type =
  | L:
     res:resource ->
     mtree 0 (hash res)
  | N:
     #n:nat ->
     #hl:hash_t ->
     #hr:hash_t ->
     left:mtree n hl ->
     right:mtree n hr ->
     mtree (n + 1) (hash (concat hl hr))

In our previous examples like vectors, the index of the type abstracts, or summarizes, some property of the type, e.g., the length. This is also the case with mtree, where the first index is an abstraction summarizing only the height of the tree; the second index, being a cryptographic hash, summarizes the entire contents of the tree.

Accessing an element in the tree

A resource identifier resource_id is a path in the tree from the root to the leaf storing that resource. A path is just a list of booleans describing whether to descend left or right from a node.

Just like a regular binary tree, it’s easy to access an element in the tree by specifying its resource_id.


Implement a function to access an element in a mtree in given a rid : list bool. Figuring out its type, including its decreases clause, is the most interesting part. The function itself is straightforward.

Exercise file


let resource_id = list bool

let rec get #h 
            (tree:mtree (L.length ri) h)
  : Tot resource (decreases ri)
  = match ri with
    | [] -> L?.res tree
    | b::ri' ->
      if b then
	get ri' (N?.left tree)
	get ri' (N?.right tree)

The Prover

Unlike the ordinary get function, we can define a function get_with_evidence that retrieves a resource from the tree together with some evidence that that resource really is present in the tree. The evidence contains the resource identifier and the hashes of sibling nodes along the path from root to that item.

First, we define resource_with_evidence n, an indexed type that packages a res:resource with its rid:resource_id and hashes:list hash_t—both rid and hashes have the same length, which is the index of the constructed type.

The function get_with_evidence is similar to get, except as it returns from descending into a child node, it adds the hash of the other child node to the list of hashes.

type resource_with_evidence : nat -> Type =
  | RES:
      res:resource ->
      ri:resource_id ->
      hashes:list hash_t { L.length ri == L.length hashes } ->
      resource_with_evidence (L.length ri)

/// Retrieves data refereces by the path, together with the hashes
/// of the sibling nodes along that path
let rec get_with_evidence (#h:_)
                          (tree:mtree (L.length rid) h)
  : Tot (resource_with_evidence (L.length rid))
	(decreases rid)
  = match rid with
    | [] ->
      RES (L?.res tree) [] []

    | bit::rid' ->
      let N #_ #hl #hr left right = tree in
      let p = get_with_evidence rid' left in
      if bit then
	let p = get_with_evidence rid' left in
	RES p.res rid (hr :: p.hashes)
	let p = get_with_evidence rid' right in
	RES p.res rid (hl :: p.hashes)

In the cryptographic literature, this function is sometimes calles the prover. A RES r ri hs is a claimed proof of the membership of r in the tree at the location specified by ri.

Going back to our motivating scenario, artifacts distributed by our content provider would be elements of the type resource_with_evidence n, enabling clients to verify that a given artifact is authentic, as shown next.

The Verifier

Our next step is to build a checker of claimed proofs, sometimes called a verifier. The function verify below takes a p:resource_with_evidence n, re-computes the root hash from the evidence presented, and checks that that hash matches the root hash of a given Merkle tree. Note, the tree itself is irrelevant: all that’s needed to verify the evidence is the root hash of the Merkle tree.

let verify #h #n (p:resource_with_evidence n) 
                 (tree:mtree n h)
  : bool
  = compute_root_hash p = h

The main work is done by compute_root_hash, shown below.

  • In the first branch, we simply hash the resource itself.

  • In the second branch, we recompute the hash from the tail of the path, and then based on which direction was taken, we either concatenate sibling hash on the left or the right, and hash the result.

let tail #n (p:resource_with_evidence n { n > 0 })
  : resource_with_evidence (n - 1)
  = RES p.res (L.tail p.ri) (L.tail p.hashes)

let rec compute_root_hash (#n:nat)
                          (p:resource_with_evidence n)
  : hash_t
  = let RES d ri hashes = p in
    match ri with
    | [] -> hash p.res

    | bit::ri' ->
      let h' = compute_root_hash (tail p) in
      if bit then
        hash (concat h' (L.hd hashes))
        hash (concat (L.hd hashes) h')

Convince yourself of why this is type-correct—refer back to the description of vectors, if needed. For example, why is it safe to call L.hd to access the first element of hashes?


Now, we can prove our main correctness theorem, namely that get_with_evidence returns a resource with verifiable evidence.

// Correctness theorem: 
// Using get_with_evidence's with compute_root_hash correctly
// reconstructs the root hash
let rec correctness (#h:hash_t)
                    (tree:mtree (L.length rid) h)
  : Lemma (ensures (verify (get_with_evidence rid tree) tree))
          (decreases rid)
  = match rid with
    | [] -> ()
    | bit::rid' ->
      let N left right = tree in
      if bit then
	correctness rid' left
	correctness rid' right

The proof is a simple proof by induction on the height of the tree, or equivalently, the length of the resource id.

In other words, evidence constructed by a honest prover is accepted by our verifier.


The main security theorem associated with this construction is the following: if the verifier can be convinced to accept a resource with evidence of the form RES r rid hs, and if the resource in the Merkle tree associated with rid is not r, then we can easily construct a collision on the underlying cryptographic hash. Since the hash is meant to be collision resistant, one should conclude that it is at least as hard to convince our verifier to accept incorrect evidence as it is to find collisions on the underlying hash.

We start by defining the type of a hash_collision, a pair of distinct strings that hash to the same value.

type hash_collision =
  | Collision :
      s1:string ->
      s2:string {hash s1 = hash s2 /\ not (s1 = s2)} ->

The security theorem shown below takes a tree and p:resource_with_evidence n, where the refinement on p states that the verifier accepts the evidence (verify p tree) although the resource associated with p.ri is not p.res: in this case, we can build a function, by induction on the height of the tree, that returns a hash collision.

 * If [verify] can be tricked into accepting the evidence of [p] when
 * [p.res] is not actually present in the tree at [p.ri], then
 * we can exhibit a hash collision
let rec security (#n:nat) (#h:hash_t)
                 (tree:mtree n h)
                 (p:resource_with_evidence n {
                   verify p tree /\
                   not (get p.ri tree = p.res)
  : hash_collision
  = match p.ri with
    | [] -> Collision p.res (L?.res tree)
    | bit::rid' ->
      let N #_ #h1 #h2 left right = tree in
      let h' = compute_root_hash (tail p) in
      let hd :: _ = p.hashes in
      if bit then
	if h' = h1 then
	  security left (tail p)
	else (
          String.concat_injective h1 h' h2 hd;
          Collision (concat h1 h2) (concat h' hd)
	if h' = h2 then
	  security right (tail p)
	else (
          String.concat_injective h1 hd h2 h';
	  Collision (concat h1 h2) (concat hd h')

We look at its cases in detail:

  • In the base case, it’s easy to construct a hash collision directly from the differing resources.

  • Otherwise, we recompute the hash associate with the current node from the tail of the evidence presented, and the two cases of the left and right subtrees are symmetric.

    • If the recomputed hash matches the hash of the node, then we can generate a collision just by the induction hypothesis on the left or right subtree.

    • Otherwise, we can build a hash collision, relying on String.concat_injective, a lemma from the library stating that the concatenation of two pairs of equal length strings are equal only if their components are. Knowing that h' <> h1 (or, symmetically, h' <> h2) this allows us to prove that the concatenations are unequal, although their hashes are, by assumption, equal.


Implement a function to update an mtree at a given rid:resource_id with a new resource res:resource. The resulting tree will have a new root hash, so you will have to return the new hash along with the updated tree.

Exercise file


One type of the update function could be as follows:

type mtree' (n:nat) =
  | MTree : h:hash_t -> mtree n h -> mtree' n

val update_mtree'  (#h:hash_t)
                   (tree:mtree (L.length rid) h)
   : mtree' (L.length rid)


let rec update_mtree' #h 
                      (tree:mtree (L.length rid) h)
   : Tot (mtree' (L.length rid))
         (decreases rid)
   = match rid with
     | [] -> MTree _ (L res)
     | hd :: rid' -> 
       if hd
       then (
         let MTree _ t = update_mtree' rid' res (N?.left tree) in
         MTree _ (N t (N?.right tree))
       else (
         let MTree _ t = update_mtree' rid' res (N?.right tree) in
         MTree _ (N (N?.left tree) t)

One interesting part of our solution is that we never explicitly construct the hash of the nodes. Instead, we just use _ and let F* infer the calls to the hash functions.

Summary and Further Reading

In summary, we’ve built a simple but powerful authenticated data structure with a proof of its correctness and cryptographic security.

In practice, Merkle trees can be much more sophisticated than our the most basic one shown here. For instance, they can support incremental updates, contain optimizations for different kinds of workloads, including sparse trees, and be implemented using high-performance, mutable structures.

You can read more about various flavors of Merkle trees implemented in F* in the following papers.

  • EverCrypt, Section VII (B), describes a high-performance Merkle tree with fast incremental updates.

  • FastVer describes the design and use of hybrid authenticated data strutures, including sparse Merkle trees, for applications such as verificable key-value stores.