Think of both trees as a heap representation (without heap properties), where the index of the root is 1, and index of a left child is (2 x index of its parent), and index of a right child is (1+ index of left child). Then traverse one tree in BFS fashion, at each node, do a BS on the second tree. If found, compare their indices.
The index can be calculated on the fly during traversing and BS, so you don't really need to copy the tree to an array or something.
This is just a theory in my head. I haven't really written code to prove it works.