Tuberculosis (TB) is a significant disease for both humans and animals worldwide. The genus Mycobacterium includes several species that cause TB disease in humans and other animals. Amongst the members of the Mycobacterium tuberculosis complex (MTC), M. tuberculosis is mainly a human pathogen, whereas M. bovis has a broad host range and is the principal agent responsible for TB in domestic and wild mammals. M. bovis also infects humans, causing zoonotic TB through ingestion, inhalation. M. bovis accounts for only a small percentage of the reported cases of TB in humans. In recent years, TB in farmed deer has become a disease as public health importance in several countries. Nowadays, there has been rapid outbreak of bovine TB in cattle and deer in Korea. Investigations are needed to elucidate the relative importance of M. bovis on TB incidence in humans, especially in Korea where bovine TB remains a problem. Also, the human sources as the cause of animal infection, M. tuberculosis from the farm workers also important for TB control of animals in Korea. Differentiation between the causative organisms may only be achieved by sophisticated laboratory methods involving bacteriological characteristics, biochemical properties, and routine resistance to pyrazinamide (PZA). M. bovis shows inherently resistant to PZA whereas M. tuberculosis is susceptible to PZA. In this study, we developed a multiplex-PCR assay based on a 12.7-kb fragment for the differential detection of M. bovis and M. tuberculosis. A total of 131 M. tuberculosis complex isolates were randomly obtained from cattle and deers that were PPD positive. they all yielded M. bovis. M. tuberculosis was not isolated from animals. and, a total of 25 M. tuberculosis complex isolates which is resistant to PZA were obtained from patient. PZA resistant MTC in humans was caused entirely by M. tuberculosis. The multiplex-PCR protocol was highly species-specific and time saving for identification of M. bovis and M. tuberculosis. This multiplex-PCR assay will be easily used as a routine monitoring tool in veterinary and medical laboratories.