Identification of commonly available Indian mud crabs of the genus Scylla was carried out using RAPD and PCR-RFLP to resolve the taxonomic ambiguity of the genus. Samples were collected from western, eastern, and Andaman coastal waters of India. A total of 16 potential species-specific RAPD markers were identified from 179 individuals using 4 arbitrary primers (OPA2, OPA14, UBC122, and UBC456). Three PCR-RFLP markers were developed that could be used to confirm taxonomic status of Indian mud crab species. The species-specific RAPD markers and the digestion pattern of PCR-RFLP analysis indicate conclusively that only 2 species of mud crabs (Scylla serrata and Scylla olivacea) are commonly present in Indian coastal waters.