Species and genetic diversity of the migrant Brachidonte spharaonis bivalve were studied along the Egyptian waters in order to determine the phylogenetic status of the species and to detect speciation with geographical isolation. Samples were collected from the Red Sea, Mediterranean Sea and Suez Canal. Genetic diversity was estimated using the DNA barcoding technique for mitochondrial CO1 gene. The DNA barcoding results showed that B. pharaonis collected from different localities were clustered in different clades indicating that the B. pharaonis population in the Egyptian coasts might form a cryptic species complex rather than a population of one species. These results may have a great impact on the conservation and fisheries status of B. pharaonis in the Egyptian waters.