This review summarized recent findings on lineage-specific characteristics of Mycobacterium tuberculosis. M. tuberculosis is more generically diverse than previously assumed, and it is expected that such genetic diversity may influence on both clinical and epidemiological aspects of tuberculosis diseases. In Japan, approximately 75% of clinical isolates belongs to the Beijing family genotype, which is highly prevalent throughout East Asia. Beijing strains have been emerging in some other areas with drug resistance and genetic homogeneity, suggesting their selective advantages over other lineages of M. tuberculosis. More frequent distribution of modern type of Beijing strains among both younger and homeless people in Japan may reflect their recent epidemics. Further studies are needed to reveal the mechanisms underlying the lineage-specific characteristics, and these will offer new insights into future tuberculosis control.