Objective To explore and analyze genetic mutations of phospholipase C (PLC)-encoding genes plcABCD among clinical isolates of Mycobacterium tuberculosis and to provide scientific basis for understanding virulence and pathogenesis of Mycobacterium tuberculosis. Methods A total of 102 isolates from patients with active tuberculosis were identified. Bacterial DNA was extracted. All plcABCD genes were amplified by polymerase chain reaction (PCR) and checked for deletions or mutations by agarose gel electrophoresis. Results According to presence or absence of plcABCD genes, 102 isolates were divided into 13 genotypes. Thirty-one (30.39%) isolates were plc wild genotype with all plcABCD genes; 71(69. 61%) isolates were plc mutant type with different plc gene deletions. Of 71 plc mutant isolates, 48 missed only one of four plc genes, 14 had deletions of 2 plc genes, 8 were triple mutants and 1 was quadruple mutant. There were 61 (59. 80%) isolates with plcD gene mutation, while the mutation rates of plcA, plcB and plcC genes were lower, which were 15. 69%(16/102), 9. 80%(10/102) and 16. 67%(17/ 102), respectively. Conclusion This study shows great diversity in plcABCD genes among clinical isolates of Mycobacterium tuberculosis, with the most common of plcD.