Caspian roach is regarded as a valuable bony fish that has economic importance in southern parts of Caspian Sea. Investigations show that natural reproduction of this species has been declining during recent years. Restocking of this fish is achieved by the way of artificial reproduction. Loss of genetic stock of this species is of great concern. In the current study, in order to study the population structure of roach, 54 individuals were captured from Gomishan and Anzali wetlands (27 individuals from each region) in April 2007. Genomic DNA was extracted using phenol-chloroform method and investigated by 10 microsatellite loci. The genetic diversity of two regions [(Gomishan: average number of alleles, Na= 11.4, average effective number of alleles, Ne= 7.92, observed heterozygosity, Ho= 0.69 and expected heterozygosity, He= 0.85) (Anzali: Na= 10.2, Ne= 7.38, Ho= 0.71 and He= 0.84)] were not statistically different (P>0.05). Analysis of molecular variance showed high genetic diversity (%95) within populations. The Fst value was 0.046, indicating low genetic differentiation among Anzali and Gomishan regions. In this study, 10 of 20 (10 loci × 2 populations) tests showed significant deviation (P≤ 0.005) from Hardy-Weinberg equilibrium due to the heterozygosity deficiency. Results from UPGMA cluster analysis, based on Nei´s genetic distance, showed that the regions are probably separated from each other.