Mycobacterium bovis, which has a broader host spectrum as opposed to Mycobacterium tuberculosis that generally causes disease in humans, mainly leads to chronic progressive pulmonary disease in a large number of domestic and wild mammals, particularly cattle. The term "zoonotic tuberculosis (TB)" is used to describe M. bovis infection in humans. "Zoonotic TB" can not be differentiated clinically, radiologically or pathologically from TB caused by M. tuberculosis. The aim of this study was to evaluate the role of M. bovis in epidemiology of human TB in Aegean Region, Turkey and to determine M. bovis genotypes responsible for human TB. Thirteen M. bovis isolates identified by spoligotyping from 482 M. tuberculosis complex isolates obtained from clinical specimens sent for routine mycobacteriological examination to the Mycobacteriology Laboratory in Medical Microbiology Department of Ege University Faculty of Medicine Hospital between 2009 and 2014 were included in the study. Drug susceptibility tests of the isolates were performed by the BACTEC MGIT 960 automated system. It was determined that 9 (63.6%) of the 13 spoligotyped M. bovis isolates in this study were ST685 (SB0288), 1 (7.7%) was ST 1118 (SB0989) and 1 (7.7%) was ST820 (SB0856), for two isolates there were no registered data in SpolDB4 and Mbovis. org databases. All the isolates were susceptible to first-line antituberculosis drugs. It was determined that 13 M. bovis isolates examined in the study accounted for 2.7% of the 482 M. tuberculosis complex isolates spoligotyped in the same period. In this study, it was determined that 8 (%61.5) of 13 patients was male, 5 (38.5%) of them was female, 9 (69.2%) of the 13 patients had pulmonary TB and 4 (30.8%) had extra pulmonary TB. Seven of nine patients with pulmonary TB and two of the four patients with extrapulmonary TB were living in the rural area, and two patients with pulmonary TB had occupational exposure. Although ST683 (SB0140) is widely seen in the world among human isolates, it was not detectedin this study and other studies conducted in Turkey. In contrast, ST685 (SB0288) and ST1118 (SB0989), which have been reported very few in the world, found to be predominant in this study. This result suggested that they may be unique spoligotypes emerging in Anatolia. In conclusion, collaborative molecular epidemiological studies are needed in conjunction with researchers working in medicine and veterinary fields to determine precisely the importance of zoonotic TB in human TB in our country, to determine the route of transmission to humans and risk factors for zoonotic TB infections, to identify the dominant types between humans and animals and to understand the phylogeographic relationships of the strains in our country.