The objective of this study was to analyse the population genetic structure of the Persian sturgeon (Acipenser persicus) in Sefidrud and Gorganrud rivers watershed based on the characterization of microsatellite markers during 2006 – 2008. 100 samples of Persian sturgeon were collected from two regions. Four microsatellite loci ( Ls 68 , Spl 168 , Spl 173 and Afu 68 ) were analyzed for the molecular characterization of this species which resulted in polymorphic patterns. DNA bands were analysed using Biocapt and GenAlex software package. A total of 109 alleles were observed of which the maximum number of alleles (17) were found in Spl168 locus which belonged to sturgeons from Sefidrud river^,s watershed and the minimum number of alleles (10) in Ls68 locus belonging to the sturgeons from Gorganrud river^,s watershed. Results of microsatellite analysis revealed that the differences between samples of two regions were not statistically significant (p>0.05), neither for the average number of alleles per locus nor for observed heterozygosities. The calculated F_st and R_st between two regions was 0.07 and 0.17 showing that the genetic difference was significant (p< 0.01). Samples from Sefidrud river^,s watershed in Spl173, Afu68 and Spl168 loci and samples of other regions in Afu68 and Spl168 loci were at Hardy-Weinberg equation. The genetic distance was calculated as 0.4 which represents a significant genetic difference between samples of two studied areas. I n conclusion, this study suggests that the Persian sturgeons in two regions of the southern part of the Caspian Sea are genetically differentiated, therefore fisheries management of these unique stocks for restocking and conservation of gene pools is highly recommended.