Rainbow trout, Oncorhynchus mykiss is the most important cold water farmed fish as a nonindigenous species in Iran. Eyed eggs have been imported from different countries to Iran. In this study, genetic diversity of 50 fish (male and female) from Iranian generation and 24 fish from French generation were evaluated. Six microsatellite markers including OMM1019 ،OMM1036 ،OMM1307 ، OmyFGT5TU ،Omy77DU and Omy207UoG were applied. Average number of observed alleles in the Iranian and the French stocks were 6.68 and 6.83, respectively. Average number of effective alleles in the Iranian and French stocks were 3.13 and 3.45, respectively. Mean expected and observed heterozygosis was 0.68, 0.53 and 0.71, 0.61 in Iranian and French stocks, respectively. The results showed significant deviation from Hardy-Weinberg equilibrium at the most of loci × stock. Fixation index Fst calculated based on allelic frequency between two stocks was 0.058 with significant difference between 2 stocks. The results of this study showed insignificant genetic differentiation based on six microsatellite loci
