The genetic polymorphism of the pike perch Sander lucioperca, sampled on the territory of the Republic of Kazakhstan (Lake Balkhash, Urals River, Syrdarya River and Shardara water reservoir, North Aral Sea) and in the Volga River, and the bersh Sandler volgensis (Lake Balkhash, Volga River) populations was examined at six microsatellite loci and the mitochondrial DNA cytochrome b gene. All examined loci were successfully amplified in both species and produced quite different allele profiles, which allows them to be used for accurate species identification of pike perch and bersh. At the same time, neither nuclear nor mitochondrial markers revealed statistically significant differentiation between the examined pike perch samples, excluding some isolation of the population from Volga River.