Over recent decades, wild reindeer (Rangifer tarandus) populations in European Russia have been exposed to significant anthropogenic pressure, resulting in range reduction and fragmentation. To understand the adaptive mechanisms and sustainability of this red-listed species under these circumstances and to work out effective conservation strategies, knowledge of the genetic structure and diversity of its population in different parts of its range is necessary. The phylogeographic structure and genetic diversity of the wild forest reindeer subspecies in the Republic of Karelia were studied based on polymorphism of mitochondrial DNA (mtDNA). The studies showed that the genetic patterns in the wild forest reindeer population were determined by historical dispersal processes and the impact of reindeer husbandry in adjacent regions. In total, 25 haplotypes of the mtDNA control region have been described, 12 of which had not been reported before and 13 have been previously obtained for wild and domestic reindeer in Russia, Finland, and Norway. The population of the subspecies in Russian Karelia is characterized by high genetic diversity both for the entire sample and for most individual subpopulation groups. The genetic distances between territorial groups of wild forest reindeer in the republic do not indicate differentiation between the Topozerskaya, Pongoma-Kuzemskaya, KuhmoKamennoozerskaya, and Nyukozerskaya groups. Phylogenetic reconstruction with reference to GenBank data showed that the haplotypes we obtained belong to two previously described reindeer haplogroups. Most haplotypes (H = 16; 65 %) fall in the widespread ancestral haplogroup III, and the rest in the West Eurasian haplogroup I. The structure of the median-joining network demonstrates a lack of differentiation between these two haplotype clades territory-wise.