The main objective of this study was to assess genetic comparison of two migratory forms of Caspian trout Salmo trutta caspius namely fall-run and spring-run. Owing to the lack of information on its genetic differences, 5 microsatellite loci were used for 58 sample analyses. Genomic DNA was extracted from caudal fin using Roche DNA extraction kit and each PCR reaction was performed in a 25 µl reaction volume. Results revealed that the most allelic frequencies were observed in fall-runs of Caspian trout. The average 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 HardyWeinberg equilibrium. Furthermore except Str543INRA in spring runs, expected heterozygosity in all loci was more than observed heterozygosity. In conclusion microsatellite loci polymorphism in this study reveals low genetic differentiation between fall-runs and spring-runs. In order to increase gene flow between Caspian trout populations of different rivers and to increase the production of these fishes, restoration of rivers habitats, as well as using more breeders originating from various rivers is highly recommended.