Common carp (Cyprinus carpio) is regarded as one of the economically important bony fish species in south Caspian Sea. In recent decades, stock rebuilding programs of common carp were carried out by artificial propagation of wild caught broodstocks that might disturb genetic diversity. In this study, 56 fish were collected from Gharahsu and Anzali regions (28 samples in each region) to investigate the populations’ structure. DNA were extracted by phenol‌-chloroform method and investigated for 8 microsatellite loci. Results showed that the range of allel number, expected and observed heterozygosity, were 11-18, 0.90 and 1.00, respectively. The analyses of molecular variance showed high genetic diversity (99%) within populations. The Fst value was 0.017 which indicates the low genetic differentiation between the Gharahsu and Anzali populations that could be because of the natural migration of fish. 13 out of 16 investigated tests showed significant deviation from Hardy-Weinberg equilibrium (p<0.05), mostly due to the excess of heterozygosity. UPGMA cluster analysis based on Nei genetic distance showed there are two different populations inhabited in these regions. The results could be of interest for management and conservation programs of this valuable species in the Caspian Sea.