The aim of this study was to determine the Beijing/W family and major phylogenetic clades of Mycobacterium tuberculosis strains of tuberculosis patients in a city with a tuberculosis incidence higher than the country average. A total of 220 M. tuberculosis strains isolated over a period of more than four years were typed by spoligotyping. Spoligotyping resulted in 64 different patterns, 38 (17.3%) of which were unique, and 26 were clusters including 182 (82.7%) strains. The major shared types were ST 53 (n = 55, 25%), ST 41 (LAM7-TUR; n = 19, 8.6%), and ST 284 (n = 15, 6.8%). The major clades observed ranked in the following order: ill-defined T superfamily (n = 112, 50.9%); Latino-American-Mediterranean (LAM; n = 33, 15%); Haarlem (n = 24, 10.9%); and the S family (n = 9, 4.1%). Three strains were in the Beijing family. A high number of strains (33 strains) showed patterns that did not fall within any of the major clades described. M. tuberculosis strains in Malatya have both STs showing a widespread distribution over the world and those restricted to this city, confirming the highly diverse nature of tuberculosis. Our results suggest that the Beijing clade, which is more prevalent among the strains with MDR and isoniazid resistance, is currently not a problem in Eastern Turkey.