Aim and Background: Rachycentron Canadum is one of the most important commercial species in the Persian Gulf.  This study focuses on molecular investigation of mentioned species in order to find and introduce the genetic differentiations and also probable genotypes for monitoring and managing the genetic resources of populations in three major catch areas in the Persian Gulf and the Oman Sea.

Materials and methods: 120 individuals of this species were caught from the northern part of the Persian Gulf and Oman Sea. DNA extraction was performed from the dorsal part of the fin of 54 Individuals using Phenol-Chloroform method. Polymerase chain Reaction (PCR) was performed using a set of primers which designed based on NADH dehydrogenase (ND2) gene.

Results: The haplotype diversity from the populations of Bushehr 0. ± 0, Sistan Baluchestan 0. ± 0.3 and mean diversity was recorded 0. ± 0.015. Also haplotype diversity from the populations of Khuzestan and Hormozgan were 0. ± 0.04 and 0. ± 0.04 respectively and the mean diversity was recorded 0. ± 0.04. haplotype diversity from the populations of Khuzestan and Bushehr were 0. ± 0.04 and 0. ± 0 respectively and the mean diversity was recorded 0. ± 0.02.

Discussion: The study showed that some haplotypes of the populations belonging to Khuzestan were setting in one clade with common ancestor compared with the other population (Bushehr, Hormozgan and Sistan population) shown in another clade indicating that restricted genetic flow between Khuzestan and other studied areas. This study confirmed that several factors including barriers (mangrove forests) and marine currents can have an effect on the population diversity of this species in the Persian Gulf and Oman Sea.