Tuberculosis (TB) remains a worldwide healthcare concern and has been characterized as an epidemic by World Health Organization (WHO). In the last few decades, DNA fingerprint techniques have become available to study the transmission of TB and other mycobacterial infections. The main gold standard typing technique is restriction fragment length polymorphism, which is widely used for molecular epidemiology purposes. However, other recently introduced techniques such as spoligotyping and MIRU-VNTR are also widely used. This review briefly summarizes the recent achievements in TB epidemiology associated with the introduction of molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex mycobacteria. Besides, in this article, the application of molecular methods in the study of epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.