A comparative molecular epidemiological analysis of the population structure of Mycobacterium tuberculosis in Mongolia and the neighboring regions of Russia was conducted. The aim was the determining of mutual influence the TB in the studied countries. Selected samples of the Mongolian (309 strains) and Russian (933 strains) cohorts of Mycobacterium tuberculosis were carried out based on the results of genotyping (used deletion analysis for RD 105/207, MIRU-VNTR 24 genotyping and subtyping of the clone CC2/W148 by the specific deletion in the kdpD gene). The results of the study indicate the isolation of transmission of TB infection in Mongolia, despite the activity of the historically formed migration between Mongolia and Russia: in the studied territories, the genotypic spectrum is qualitatively different. The subtypes CC1, CC2 and BL7 of the genotype Beijing predominate in the Russian territories (Buryatia, Zabaykalsky Krai and Irkutsk Region), and the CC4 subtype of the genotype Beijing presents in Mongolia (64.5%). The molecular genetic structure of Mycobacterium tuberculosis has no significant differences in the borderlands with Russia and in the central provinces of Mongolia.