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Tuberculosis (TB) is a major public health concern in Qinghai which located in the northeastern region of Qinghai-Tibet Plateau and characterized by low oxygen and low pressure. This study was conducted to explore the genotypes of Mycobacterium tuberculosis (MTB) in this high altitude region. A total of 251 MTB strains were collected and genotyped by spoligotyping and 15- loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of 251 MTB isolates revealed 49 distinct spoligotype patterns and Beijing lineage was found to be the most dominant MTB strain including 74.0% (185/251) of total isolates. 217 isolates grouped into 15 clusters with the clustering rate of 86.5% (217/251). While 15-loci MIRU-VNTR distributed 251 isolates into 4 groups containing 238 different MIRU-VNTR profiles, Group II was the largest group representing 91.9ï¼ÂÂÃ‚Â… (230/251) of isolates. Clustering rate by MIRUVNTR was 85.7% (215/251). Spoligotyping and MIRU-VNTR matched well in lineage classification. We concluded that 15-loci MIRU-VNTR has more abundant diversity than spoligotyping and would be useful to trace transmission routes and sources of infections.