Rybnikova, Naryan-Mar, Nenets Autonomous District, 166004 Russia, e-mail nmshos@atnet.ru; 5Institut fьr Tierzucht und Genetik, University of Veterinary Medicine (VMU), Veterinдrplatz, A-1210, Vienna, Austria, e-mail gottfried.brem@agrobiogen.de Acknowledgements: Supported by Russian Science Foundation (project ¹ 16-16-10068) Received September 5, 2016 A b s t r a c t The coexistance of domestic and wild reindeer populations (Rangifer tarandus L., 1758) — is an important feature of this species. <...> Due to gene flow between domestic and wild populations we observe a relatively high amount of admixture in the gene pool. <...> Biodiversity characteristics of two most numerous reindeer populations (semi-domesticated Nenets breed and wild population of reindeer inhabiting territories of Nenets Autonomous Okrug (NAO) and Taimyr Autonomous Okrug (TAO) based on the analysis of microsatellites are given and the degree of introgression in these populations is determined. <...> Samples of Nenets breed of domestic rein deer were collected in several farms in NAO and TAO (n = 115, four subpopulations). <...> Genomic DNA was isolated using Nexttec columns («Nexttec Biotechnologie GmbH», Germany). <...> To estimate the allele pool of each population average number of alleles (Na), the effective number of alleles (Ne) based on the locus, rarified allelic richness (Ar), private allelic richness (PrAr), observed (Ho) and expected (He) heterozygosity and inbreeding coefficient (FIS) were calculated. <...> The degree of genetic differentiation of populations was assessed using pairwise FST values and Nei’s genetic distances. <...> We calculated the degree of migration of genes between populations based on microsatellite allele frequencies. <...> It was found that the wild population of reindeer is characterized by a higher level of genetic diversity: the average number of alleles per locus was 10.00±0.78 vs. 8.44±0.80, the observed heterozygosity — 0.633±0.060 vs. 0.589±0.049. <...> However, a few individuals (4.4-4.8 %) carrying a mixed genetic origin were found. <...> Cluster analysis of genetic structure performed separately for wild and domestic populations at the level of subpopulations for the number of cluster k ranged from 2 to 5 did not reveal a clear clustering between subpopulation. <...> It’s confirmed the homogeneity of genetic structure within populations. <...> Examination <...>