The Caspian salmon S. trutta caspius in respect to its reproductive life cycle has two immigrant forms namely fall-run and spring-run. As the Shahid Bahonar center activities on Caspian salmon stocks restoration in Klardasht of Iran has been just focused on fall-run form propagation, it could be proposed that these stocks proportions have been gradually increased. Regarding to lack of information on genetically differences between the two groups, in this study, genetic structure of these immigrant forms were analyzed by using 5 microsatellite loci. Results revealed that the most allelic frequencies were observed in fall-runs. Average of observed and expected heterozygosity in fall-runs and spring-runs were, 0.7719, 0.6108 and 0.4435, 0.5911, respectively. In both groups except Str543INRA in spring runs, all loci had deviation from Hardy-Weinberg equilibrium. Furthermore except Str543INRA in spring runs, expected heterozygosity in all loci was more than observed heterozygosity. Genetic distance between two populations and Fst, as a population distinctive index, were 0.081 and 0.025, respectively. In conclusion 5 microsatellite loci used in this study show low genetic differentiation between fall-runs and spring-runs