Mycobacterium bovis is the main causal agent of bovine tuberculosis (BTB) that causes zoonotic tuberculosis (TB) in humans, even though M. caprae; contribute to a lesser extent, which is mostly acquired from domestic animals and their products, in which cattle are the major reservoir. This review paper discussed the importance of zoonotic tuberculosis in Africa and highlighted the uses of molecular methods in diagnosis, control and prevention of zoonotic tuberculosis. Despite the fact, there are various diagnostic methods available nowadays; the molecular techniques are proving more rapid and plausible sensitivity and specificity results that increase the diagnosis precision. In addition, molecular diagnostic methods used to indicate the epidemiological status of different strain distribution with regard to cluster distribution and reactivation of dormant or treated cases of tuberculosis indicating the drug resistance situation of the strain. Hence, applying molecular techniques for diagnosis of zoonotic tuberculosis in developing countries will help in decreasing the incidence, prevalence, mortality, morbidity and loss of economic due to carcass condemnation, milk drop and livestock trade banning in the continent. Advanced molecular methods truly play a key role in prevention and control program of tuberculosis in general and bovine tuberculosis in specific, which leads to the cooperation of various disciplines. Introducing cost effective and easy molecular diagnostic methods is recommended, implementing molecular diagnostic methods in research areas and intensive training of personnel in the use of equipment.