Rainbow trout ( Oncorhynchus mykiss ) is the most important cold water fish farmed in Iran. In this study the population structure of cultivated stocks of rainbow trout was analyzed using 10 microsatellite loci namely OMM1378, OMM1379, OMM1380, OMM1382, OMM1384, OMM1386, OMM1396, OMM1399 andOMM1402. A total of 204 fin clip samples were obtained from eight hatcheries (West Azarbaijan (WA), Tehran, Chaharmahal and Bakhtiari (ChB), Fars, Qazvin, Kohgiluyeh and Boyer-Ahmad (KB), Lorestan and Mazandaran). DNA was extracted using ammonium acetate method. The electrophoresis of polyacrylamide gel 12% was performed and silver staining method was used for visualizing the PCR products. The average observed allele frequency and heterozygosity ranged from 8 to 9.8and 0.720 to 0.8 respectively. The average observed heterozygosity and allele frequency in WA, ChB, Fars, Qazvin, Lorestan, Mazandaran, Tehran and KB were 0.724, 9.8; 0.756, 8; 0.771, 8.8; 0.763, 9.6; 0.788, 9.2; 0.823, 9.8; 0.720, 9 and 0.750, 9.23 respectively. Deviation from Hardy-Weinberg equilibrium was observed in 39 out of 40 studied loci. However, after the application of Bonferroni correction, 37 loci showed deviation from Hardy-Weinberg equilibrium. The maximum inbreeding coefficient (0.136) was observed in Tehran population while Mazandaran population showed the minimum inbreeding coefficient (0.047). The maximum genetic distance (0.404) was observed between KB and WA populations whereas Mazandaran and Fars populations showed the least genetic distance (0.182). Accordingly, KB and WA populations showed the least genetic identity (0.668) while the maximum genetic identity (0.834) was observed between Mazandaran and Fars populations. The F ST was 0.011 indicating low genetic differentiation among populations. There was a genetic diversity of 98% within populations while the genetic diversity among populations accounted for only 2% of overall observed genetic diversity. The maximum genetic diversity was observed in Mazandaran population, on the other hand, ChB population showed the least genetic diversity. The results of this study demonstrated that the populations had a low inbreeding coefficient and there was a high level of genetic diversity within the cultivated stocks of rainbow trout. Keywords : genetic diversity, genetic distance, heterozygosity, microsatellite, Oncorhynchus mykis .