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Objective To evaluate the application of different variable number tandem repeats(VNTR)locus in genotyping of Mycobacterium tuberculosis strains isolated from Uygur in south of Xin-jiang.Methods 24 MLVA loci of 151 MTB strains were analyzed respectively.Results 24 loci showed different discriminatory, in which Qub 26 (HGI 0.824)、 QUB-11 b(HGI 0.816) and Mtub 21 (HGI 0.721)were the relatively more polymorphic loci.The clustering of genotype showed that these strains could be categorized into 8 gene groups and 151 genotypes according 24 loci.Conclusion Different VNTR locus and locus-set showed different discriminatory power in the selected Mycobacterium tuberculosis isolated from south ofXin jiang.Twenty-four-loci set can be used in molecular epidemiological study of Mycobacterium tuberculosis in Xinjiang after standardization.