Mycobacterium tuberculosis is an intracellular bacterium that can proliferate within phagocytosed macrophages. M. tuberculosis gains this ability by inhibiting phagolysosome biogenesis. On the other hand, autophagy induction can eliminate infected mycobacteria in macrophages. Numerous reports have demonstrated the mechanism of membrane trafficking in macrophages infected with mycobacteria to elucidate how M. tuberculosis proliferates within macrophages. In this review, we make a commentary on the molecular dissection of M. tuberculosis-containing phagosomes demonstrating which host factors constitute the replication niche for mycobacteria, and approach the real images of mycobacterial phagosomes.