The aim of present study was to compare levels of genetic polymorphism between offspring of  wild , farmed and mix of them of Roach (Rurilus rutilus caspicus) using five microsatellite loci  (CA1, CA7, CypG27, Lid1, Rru4). Genetic diversity was investigated by studying samples collected from three population, 90 fish, thirty specimen form each population. All samples fixed in ethanol 96% until DNA extraction. The average number of alleles in wild, farmed and mixed brood stock offspring were 10.4 and 10.4 and 9 alleles, respectively. A twenty nine total alleles were observed in all three populations. The numbers of effective alleles of wild, farmed and mixed offspring were 6.78, 7.58 and 6.80 alleles in each population, respectively. The Allele frequency among wild, farmed and mixed population were 7, 8 and 8, respectively.  All frequency decline in wild fish due to inbreeding and genetic drift. The mean of observed heterozygosis (Ho) values were 0.85, 0.77 and 0.85 in wild, farmed and mixed offspring respectively. Also effective heterozygosis (He) were 0.828, 0.859 and 0.849 in wild, farmed and mixed offspring respectively. Approximately, all of loci showed deviation from Hardy-Weinberg equilibrium. The genetic distance among of wild, farmed and mixed offspring populations were 0.459, 0.298 and 0.684, respectively. The results of Molecular Variance Analysis revealed that genetic diversity within individual was 90 percent, while among them was 3 percent. The Fst value was 0.032 that indicates the low genetic differentiation between the three populations which could be explained by the low number of alleles in three populations. Furthermore, the Natural Migration (Nm) between two stations was obtained 7.394. UPGMA cluster analysis based on genetic distance showed that the breeding population and combined in a separate branch of the branches are wild population.