The reindeer of the Tuva population inhabiting the south of Eastern Siberia and belong to one of the southernmost populations of domestic reindeer. The population census size of those reindeer was declined dramatically from 15,000 in 1990 to 1,500 individuals in 2019. A genetic study of this population is mandatory for assessing the risk of loss of its genetic diversity in order to develop the proper management strategies for preserving this unique genetic resource. In our study, we examined genetic diversity of Tuva reindeer based on both a high-density SNP genotypes analysis (n=12) and a complete cytochrome b (cytb) sequences (1,140 bp) (n=6). To find out a possible genetic contribution toward the Tuva reindeer population structure, SNP genotypes and cytb sequences of all officially recognized breeds in Russia were added to our datasets. All genetic diversity indices calculated based on both nuclear and mitochondrial genomic data were lowest in Tuva population. Median-joining network, a principal component analysis and F_ST-based Neighbor-Net tree showed that Tuva population was most distant, while other breeds formed well-separated clusters according to their geographic locations. The low level of genetic diversity of the Tuva population observed in our study, based on studies involving a genome-wide approach, as well as a complete cytochrome b sequences, indicated the need to take appropriate measures to avoid negative consequences for this domestic reindeer. This study was supported by RSF-21-16-00071 and Russian Ministry of Science and Higher Education-0445-2019-0024.