Abstract: The aims of this study were to analysis the population genetic structure and genetic diversity among and between populations of Sander lucioperca based on microsatellite markers. For this purpose, 149 samples of adult pikeperch from three regions of Southwest Caspian Sea (Talesh Coasts, Anzali Wetland and Chaboksar Coasts) were collected. DNA was extracted and using 13 pairs of microsatellite primers, Polymerase Chain Reaction (PCR) was conducted. DNA bands were analysed using Biocapt and GenAlex software package. Out of 13 microsatellite primers, 11 loci were produced, in which 6 of them were polymorphic and 5 monomorphic. Analysis revealed that the average number of alleles per locus and observed heterozygosities were not statistically significant (p>0.05) for all 3 populations. The FST value between populations was low but significant (p<0.01), suggesting that the 3 populations are genetically differentiated. Deviation from Hardy-Weinberg equilibrium was obvious in most cases, mostly due to the deficiency of heterozygosities. The highest genetic distance was between Anzali Wetland and Chaboksar Coast populations. The data generated in this study provide useful information on the genetic variation and differentiation in populations of Southwest Caspian Sea pikeperch.