Population genetic structure of stellate sturgeon (Acipenser stellatus) in 197 adult specimens from four fishery regions along the Iranian coastline of the southern Caspian Sea was investigated using microsatellite markers. Out of 15 microsatellite primers, 11 loci were produced, in which 10 of them were polymorphic and 1 was monomorph. Totally, 184 alleles were identified and on average 13.1 alleles per locus were found (ranged 8 to 18 alleles). All sampled regions contained unique alleles. Average observed and expected heterozygosity was 0.667 and 0.854, respectively and significant genetic differences between 4 regions were observed (p≤0.01). Deviations from Hardy-Weinberg equilibrium were found in most cases. Population differentiation test was modest and significant (p≤0.01). Based on FST estimate (p≤0.01), more than one population of stellate sturgeon is identified in the south Caspian Sea. Therefore, fishery management for restocking and conservation of gene pool is highly recommended.