In the present study, five pairs of microsatellite primers (C83Sc, D61Sc, H96Sc, J43Sc, L42Sc) were used to identify potential populations and to investigate the genetic diversity of Persian Gulf lion populations (Scomberomorus commerson). Lionfish samples were collected from three stations: Bandar Deir, Bushehr Port and Choobdeh Port in the northern waters of the Persian Gulf. To determine the genetic differences using these five loci, 115 samples of fish milk were used. The PCR reaction performed well with all primers and all five loci in all three populations were polymorphic. Three specific alleles in three loci for the population of Deir and one specific allele in one locus for the population of Bushehr were obtained. In the Hardy-Weinberg equilibrium study, all three populations were out of balance in all studied gene loci (P <0.001). Genetic differences were measured by the Fst index to estimate the structure of the reserves. According to AMOVA test, the lowest Fst = 0.025 was observed between Deir and Bushehr samples which had 9.818 gene flow and the highest Fst = 0.057 was observed between Deir and Choobdeh samples which had 4.164 gene flow. . The results suggest that there is probably a milkweed population in the sampled stations and that an integrated fisheries-genetic management is necessary for the sustainable use of this valuable resource.