Abstract <p>The Caspian seal (<i>Pusa caspica</i>) is the endangered endemic mammals in a closed sea and smallest earless seal. There is a great concern for Caspian seal future regarding the sharp decline of this species over the last decades. To the best of our knowledge, there is not any study that used microsatellite markers to evaluate the genetic diversity and population differentiation of the Caspian seal. In this study, genetic diversity and population structure of the Caspian seals was examined using 20 polymorphic microsatellites to investigate population genetic parameters in a long distance of the southern coast of the Caspian Sea. The mean of expected and observed heterozygosities were 0.89 and 0.87, respectively which are indicating high genetic diversity for this species. Our results showed that the inbreeding index is very low. Despite the result of STRUCTURE outputs, and DAPC analysis, there isn’t compelling evidence that Caspian seals could maintain demographically separate units, which would be necessary to give rise to genetic population structure. The longest migration route for seals from the ice breeding area is for the western population. Migration patterns in previous research may confirm this relative separation, but further research is needed to prove the fact. Based on the results, there was not any evidence of bottleneck for the East population. In conclusion, the results of this study provide helpful information for the management and effective conservation of Caspian seals. Also, it is suggesting to investigate carefully about life cycles and migration patterns of the West population.</p>