Rainbow trout ( Oncorhynchus mykiss ) a Salmonid fish is one of the most important cold water fish farmed in Iran. Considering the importance of genetic variation and population structure for management and broodstock selection for replication competent in the farms, the genetic diversity of rainbow trout was investigated using molecular techniques. In this study 204 specimens of rainbow trout were collected from eight populations (Yasouj, Fars, Lorestan, Tehran, Qazvin, Mazandaran and West Azerbaijan, Chaharmahal and Bakhtiari). For molecular study, DNA was extracted using ammonium acetate method from fin clips. The DNA quality was examined by electrophoresis on 1% agarose gel and painted with ethidium bromide. PCR amplification was performed using eleven pairs of microsatellite loci (OMM1332, OMM1377, OMM1396, OMM1385, OMM1383, OMM1376, Omy77, OMM1400, OMM1404 and OMM1392) at annealing temperatures of 51.5-62.5. The eight loci were polymorphic. PCR products were electrophoresed on 12% achrylamid gel and stained with silver nitrate(AgNo 3 ). Calculations were done using GenAlex.6 (ver. 6) and ARLEQUIN (ver. 3.11) software. The mean of different alleles was 12.531. The mean of effective alleles was 8.841 and the Shannons Information Index was 2.275. The means of observed heterozygosities in populations was 0.878 to respectively. The mean of expected heterozygosity for populations was 0.872 and the Unbiased Expected heterozygosity in populations was 0.891. Results showed deviation from Hardy-Weinberg equilibrium at 41 out of 64 studied loci. Increase of observed heterozygosity towards expected heterozygosity at Chaharmahal and Bakhtiari, Fars, Lorestan, Tehran, Qazvin, Mazandaran population. The most genetic identity in all population was 0.719 between Tehran and Mazandaran population respectively and the least of Genetic identity was 0.373 between Fars and Qazvvin population. The genetic distances in all population was ranged 0.688-0.487. The F ST was measured in the range of 0.026-0.067 and F IT in the range of -0.064-0.329. The diversity among groups was 0.89%, diversity among populations within group was 2.8% and diversity within populations was 96.31%. A tree diagram of the four populations based on Nei (1972, 1978) genetic distance and UPGMA method was performed. Based on the results Yasouj, Fars, Lorestan, Tehran, Qazvin and West Azerbaijan, Chaharmahal and Bakhtiari populations were put in a same branch while Mazandaran population was placed in separate branch. It could be a good candiate for croreeding and reproduction of Inbreeding depressian in other population. Keywords: Inbreeding, genetic variation , heterozygosity , genetic distances .
