Population genetic structure of Vimba vimba persa was investigated using microsatellite markers from 40 regions along the Iranian coastline of the Southern Caspian Sea (Anzali lagoon and Havigh River in Gilan province, BabolRoud River in Mazandaran province and GorganRoud River in Golestan province). Genomic DNA from 121 specimens was extracted from fin tissue by the Phenol-Chlorophorm method and PCR reaction was accomplished with 17 microsatellite primers, out of 17 microsatellite primers 13 loci were amplified, in which 10 of them were amplified with reasonable polymorphism and 3 were monomorphism. A total of 302 alleles were identified on average 7.55. Observed and expected heterozygosity averages were 0.80 and 0.77 respectively. Most cases significantly deviated from Hardy-Weinberg equilibrium (p≤0.01). The estimation of Fst (p≤0.01) revealed significant population structuring and an estimation of the four population of Vimba vimba persa was identified in the Caspian Sea in which restocking of these species should be considered.