A method, article of manufacture, and apparatus for managing data commonality in a Merkle tree is disclosed. Reference counts are associated with a node in the Merkle tree. Data commonality is detected and the root of the detected data commonality is determined. If a node is the root node of the detected data commonality, the nodes reference count is incremented. When an object is deleted, the root node of the object is determined. The reference count of the node is decremented. If the count reaches zero, the node is removed from the Merkle tree, and its child nodes are decremented.