Finding the common substructures shared by two proteins is considered as one of the central issues in computational biology because of its usefulness in understanding the structure-function relationship and application in drug and vaccine design.In this paper, we propose a novel algorithm called FAMCS (Finding All Maximal Common Substructures) for the common substructure identification problem. Our method works initially at the protein secondary structural element (SSE) level and starts with the identification of all structurally similar SSE pairs. These SSE pairs are then merged into sets using a modified Apriori algorithm, which will test the similarity of various sets of SSE pairs incrementally until all the maximal sets of SSE pairs that deemed to be similar are found. The maximal common substructures of the two proteins will be formed from these maximal sets. A refinement algorithm is also proposed to fine tune the alignment from the SSE level to the residue level.Comparison of FAMCS with other methods on various proteins shows that FAMCS can address all four requirements and infer interesting biological discoveries.