Kyrgyzstan is a post-Soviet country in Central Asia marked with high incidence and mortality rates of tuberculosis (TB). The present study provided first assessment of Mycobacterium tuberculosis population structure and drug-resistance in civilian population here. The collection included 103 M. tuberculosis DNA samples subjected to the analysis of rifampin and isoniazid resistance mutations and spoligotyping. The major spoligotype-defined families were Beijing (n = 62), T (n = 14), LAM (n = 9), Ural-2 (n = 6) and Ural-1 (n = 3). Genotypically, 20 isolates were RIF-resistant, 28 were INH-resistant, 17 were multidrug-resistant. Drug resistant isolates were more prevalent among Beijing than non-Beijing groups (P = 0.03). The predominance of the mainly “Russian” spoligotypes among the non-Beijing strains (LAM-RUS and Ural-1) in this study along with previously demonstrated prevalence of the Russia-specific subtype of the Beijing family in Kyrgyz prison (Mokrousov et al., 2009) suggest that the current population structure of M. tuberculosis in Kyrgyzstan has been mainly formed within the course of the 20th century when the country was a part of the Russian Empire and Soviet Union. On the other hand, a prevalence of the Asia-specific Ural-2 type in the oldest age group (68–85 years old; P < 0.0001) may present a heritage of the more distant historical events. In summary, we suggest: (i) a clear shift of the local M. tuberculosis population structure during the last 100 years and (ii) a critical impact of the Beijing genotype on the current situation with drug resistant TB in Kyrgyzstan.