Family Carangidae is widely distributed in the Atlantic, Indian and pacific Oceans. Two morphologically similar species, Trachurus indicus and Decapterus maruadsi, were collected and recognized from the Gulf of Suez. The two species have no distinct differences morphologically. Microsatellite DNA markers revealed that the populations of the two species represented distinct genetic divergence. This genetic diversity study showed that the populations of the two species are not related to each other. Overall, this study reveals high genetic diversity of T. indicus and D. maruadsi populations. Further studies on the genetic structure of these two species, are needed not only to understand the evolutionary history of the species, but also to improve the knowledge-based fishery management programs of this important biological resources.