The population structure of Rutilus rutilus caspicus (Jakowlew, 1870) from two locations on the Iranian coastline and one location in Russia was investigated using microsatellite DNA markers. Genomic DNA from 90 specimens and seven loci with reasonable polymorphism were amplified using a PCR approach The results showed that the lowest mean number of alleles per locus (6.42) was observed in the Russian population and the highest (7) in the Gorgan Bay population. The observed heterozygosity in the Anzali Wetland (0.59) population was higher than the other populations in Iran (Gorgan Bay: 0.5) and Russia (0.52). Significant to highly significant deviations from Hardy-Weinberg expectations were found at more loci in Iranian populations than in the Russian. Population differentiation was modest among all populations. The highest and significant (0.044; p≤0.01) population differentiation (F st) value was between Iranian populations and Russian populations and the lowest and non-significant population differentiation (F st) value was between Iranian populations (0.012; p≤0.07). The estimated gene flow (N m) value between Iranian populations (Gorgan Bay and Anzali Wetland) across all the studied loci was the highest, while the Nm value between Iranian and Russian population was the lowest.