Population structure of Epinephelus coioides (Hamilton, 1822), Orange-spotted grouper, was studied based on six polymorphic microsatellite loci in the Persian Gulf waters. 3-5 gr of each individual’s soft tissue were prepared through 120 hunted individuals of 4 sampling stations. DNA extraction was performed using a standard ammonium/acetate method. Quantification and quality control of DNA were done using spectrophotometery method and 1% agarose gel electrophoresis. DNA fragments was amplified via PCR and the products were run on polyacrylamide gel. Staining of the gels was performed through silver nitrate. Statistical analysis represented mean of genetic parameters include real and effective alleles, observed and expected heterozygosity for over loci in all populations, 5.458, 3.793, 0.500 and 0.649 respectively. The AMOVA test showed maximum rate of Fst (0.086) and minimum rate of Nm (2.652) between Khuzestan and Bushehr populations; Also minimum rate of Fst (0.034) and maximum rate of Nm (7.070) were between Dayyer and Bandar-Abbas populations. Khuzestan was the ultimate population and results were showed an intermediate separation from other studied populations; thereby separated fisheries management is recommended.