Pikeperches (Stizostedion lucioperca and S. volgense), river perch (Perca fluviatilis), and ruffe (Gymnocephalus cernuus) are important ichthio-fauna of Kuibyshev water reservoir in Russia. Now a days, the stock and production of these species are declining in this artificial lake. The recent declines of pikeperches has prompted the interest in assessing genetic structuring of their populations. The maintenance of genetic variation and rapidly amplified DNA polymorphism (RAPD) between the exploited fish populations, a product of past evolution in attributes to the ecology is the initiative to increase the overall chances that depleted population will regain and persist over the long period. The RAPD in Percids has a significant variation in among populations. Two microsatellites DNA from walleye (S. vitreum) were used as primers in this study. Each of the DNA markers (Svi-4 and Svi-18) resolved 4–6 alleles with a size range of 102-124 bp. The RAPD analysis revealed diversified polymorphic structures in different Percid populations. PCR products of both of the Stizostedion species have rapidly amplified DNA amplifications with a size range of 100–1200 bp. Most of the dominant DNA fractions of Percids were existed in the size range of 100–600 bp in both of the primers treatments. The Stizostedion had RAPD with a size range of 100–400 bp with 2–3 dominant DNA bands in 100, 140 and 200 bp. In pikeperches the amplified DNA bands are more or less similar, which demarked that these two species were evolved from the same phylogenetics and evolutionary origin. The river perch had only one dominant band and the ruffe had two DNA amplification signals. RAPD in different Percids depends on the specific size range of the DNA amplifications.