A Merkle tree is a structure that repeatedly hashes pairs of data until one hash remains. That final hash is called the Merkle root.
Bitcoin uses this structure for the transactions in a block. The transaction data forms the leaves of the tree. Hashes are combined in pairs, and the process continues until Bitcoin has one resulting Merkle root. Bitcoin places that root in the block header.
Why is the Merkle root in the block header?
The Merkle root acts as a compact summary of the transactions associated with that block. Bitcoin’s developer reference documents the rules used to build the tree, including the ordering and treatment of an odd final hash. Those are Bitcoin-specific construction rules, not universal rules for every blockchain.
What a Merkle tree does not mean
A Merkle tree is not the same thing as a blockchain, a block or a hash. It also does not, by itself, prove that every piece of information connected with an event is true, private or permanently available. Its role here is narrower: Bitcoin uses it to derive a Merkle root from the transactions in a block.
In short
A Merkle tree repeatedly hashes paired data to produce one Merkle root. In Bitcoin, the root is derived from a block’s transactions and stored in that block’s header.