Abstract: Objective To study the polymorphisms in pstS1 and its human T and B cell epitopes of Mycobacterium tuberculosis complex (MTBC) strains in China. Methods The pstS1 sequences of the 180 clinical MTBC isolates and 11 BCG strains were obtained by PCR and first generation sequencing, and together with the published data of one Mycobacterium bovis and 3 BCG trains, the sequences were compared with the human T and B cell epitope sequences from Immune Epitope Database (IEDB). The dN and dS values were calculated with Mega 5 software. Results Two kinds of insertion and 4 single nucleotide polymorphism (SNP) mutations were found in pstS1 gene of the studied samples, which affected 79.17% (19/24) of B cell epitopes and 65.22% (15/23) of T cell epitopes area. The dN value of whole pstS1 gene was 0.000 14, those of T epitopes and non-T epitopes areas were 0.000 17 and 0.000 05 respectively and those of B cell epitopes and non-B epitopes areas were 0.000 23 and zero. The dS value of all sequence types were zero as there was no synonymous mutation. Conclusion The polymorphisms exist in the pstS1 and its human T and B cell epitopes of the MTBC strains selected in China, and the T and B epitope regions have relatively high levels of mutation.