The population structure of Epinephelus coioides, common Hummer, in the Persian Gulf was examined for 6 polymorphic microsatellites. 3-5 grams of soft tissue of each of the 120 samples collected from 4 stations were prepared. DNA extraction was performed using the standard method of ammonium acetate and its quantity and quality were evaluated by spectrophotometry and electrophoresis on 1% agarose gel. The DNA fragments were amplified by PCR and then driven onto polyacrylamide gel and stained with silver nitrate. The mean of genetic parameters includes real and effective alleles for all loci and populations, 5.458 and 3.793, respectively, as well as observed and expected heterozygosity 0.500 and 0.649, respectively. AMOVA test showed the highest Fst (0.086) and the lowest gene flow (Nm = 2.652) between Khuzestan and Bushehr, the lowest Fst (0.034) and the highest gene flow (= 7.070). Nm) between the two populations of Dir and Bandar Abbas. The population of Khuzestan shows relative separation in comparison with other studied populations, therefore separate fisheries management practices are recommended.