Silver pomfret, Pampus argenteus, is a commercially high-value species and a good candidate for aquaculture development which is now under environmental pressure due to overfishing and other ecological changes. In the present study, population structure of silver pomfret from Oman Sea and Persian Gulf were investigated using 7 microsatellite loci and restriction fragment length polymorphisms (RFLP) of the mitochondrial ND-2 gene region. For this purpose 100 samples were collected from 4 locations (kuwaiti waters, khozestan, Bushehr and Chabahar). By using 16 restriction enzymes, the estimates of mtDNA haplotype and nucleotide diversity were (h = 0.0875 ± 0.00143, π = 0.001238 ± 0.0000004). The result for testing of homogeneity in haplotype frequencies by monte-carlo test was (χ² = 68.8, P> 0.05) which showed that a monophylitic population lives in Oman Sea and Persian Gulf. However,the average of observed and expected heterozygosity was 0.53 and 0.67 respectively. After appling the Hardy-Weinberg Equilibrium (HWE) tests, most of loci were found to deviate significantly from HWE in some populations in which deficiency of heterozygosity was apparent. Pairwse Fst valus showed significant difference between all studied populations (P<0.01). Results indicated that microsatellite markers are more powerful than PCR-RFLP in determination of genetic diversity and population structure in this species.