Rangifer tarandus L. 1758 is one of the few modern hoofed species in which domestic and wild forms coexist in the same territory. The genetic differentiation of domestic and wild reindeer in Northern Eurasia was examined using microsatellite data. А total of 780 animals were studied at 16 microsatellite loci. Samples of wild reindeer were taken from seven populations inhabiting different natural areas, and samples of domestic animals were selected from the Evenki, Evens, Chukchi and Nenets breeds, including two ecotypes, Tofalar and Todzha reindeer. The levels of genetic diversity and variation in wild reindeer were higher than in domestic ones. Bayesian clustering analysis allowed us to distinguish domesticated reindeer populations by the degree of taming, but failed to detect differences in genetic structure between wild reindeer populations. These differences were found using the pairwise Fst values. Overall, the microsatellite analysis revealed a significant genetic differentiation between domestic and wild forms and the structuring of populations within each form, which may be important for the development of strategies for animal conservation.