Abstract: Objective To study the polymorphism of the phospholipase C gene in Mycobacterium tuberculosis isolated in Qinghai and to explore its relationship with strains of Beijing family. Methods A total of 250 strains of clinical isolates of Mycobacterium tuberculosis from 2012-2016 in Qinghai were collected, multiple-locus variable-number tandem repeat analysis (MLVA) was performed for identification of Beijing and non-Beijing families, and the phospholipase C gene was analyzed by polymerase chain reaction (PCR). Results Of the 250 isolates of Mycobacterium tuberculosis, 184 strains were Beijing family accounting for 73.60%. 66 strains were non-Beijing strains accounting for 26.40%. The results showed that plc genes of Mycobacterium tuberculosis in this region were polymorphic. plcA,plcB and plcC genes were mutational in the strains with 13.20%, 15.20% and 16.40% respectively. Their mutation rates were low, while plcD gene mutation rate was as high as 97.20%. plcA,plcB and plcC mutation rates were found statistically significant between Beijing and non-Beijing strains (all P<0.05), but no difference in plcD gene (χ²=0.322, P=0.571). Conclusions The mutations of the plc gene may attenuate the virulence of Mycobacterium tuberculosis isolates, and Beijing family strains have few mutations in this gene, so that may cause the widespread of Beijing strains in Qinghai.