Reindeer (Rangifer tarandus) in Russia is presented by a number of wild and domestic populations. Both wild and domestic reindeer play an important role in lives of indigenous people. Investigation of biodiversity of this species is very important for developing conservation and breeding programs. Our research was aimed at determining haplotype variability and genetic diversity of the wild and domestic reindeer. MtDNA cytb gene (1,140 bp) of the wild reindeer from the Taimyr region (WLD, n=16) and domestic reindeer from the Nenets-Autonomous district (NEN, n=15) and Tuva Republic (TUVA, n=5) were sequenced. It was shown that the number of variable sites was higher in WLD – 35, than in NEN and TUVA – 17 and 5, respectively. Haplotype diversity was 0.958±0.036 in WLD, 0.762±0.096 in NEN and 0.900±0.161 in TUVA. Average number of nucleotide differences was 7.942 in WLD, 4.324 in NEN and 2.800 in TUVA. The median-joining network revealed that WLD and NEN had shared haplotypes with each other, while TUVA had private haplotypes. Thus, the obtained results of the current study demonstrated that the wild reindeer were characterized by higher genetic diversity than both domestic groups. Tuva reindeer clustered separately from the other populations and were characterized by higher haplotype diversity than the Nenets conspecifics that had a higher average number of nucleotide differences.