The Cuttlefish Sepia pharaonis, is an Indo–Pacific organism and is one of the most economic species in the Suez Canal fisheries. Despite its economic value, there is a shortage of taxonomical information on the species. A total of 50 specimens of cuttlefish were collected from the Suez Canal. The sampling was during the period from winter to autumn 2021. Samples were identified morphologically and genetically by using COI gene. The species showed a genetic variation between the different populations of the same species and a genetic variation from the other species of cephalopods. The molecular identification method showed a great reliability in the identification of the cuttlefish.