Region of Difference 2 (RD2) was lost during the ongoing propagation of BCG between 1927 and 1931, a time that coincides with reports of the ongoing attenuation of the vaccine. Some data demonstrate that RD2 plays a role in mycobacterial virulence, and that its deletion from Mycobacterium tuberculosis leads to a decrease in bacterial growth in both a macrophage and a murine model. Human T-cell epitopes of M. tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion. However, two antigens, Rv1986 and MPT64, encoded by RD2 harbored more than one amino acid changes. In this study, we used same set of clinical M. tuberculosis complex (MTBC) isolates from China, amplified the five genes containing T and B cell epitopes other than MPT64 encoded by RD2, and compared the sequences. It turned out that proteins in RD2 region, especially Rv1980c, Rv1985 and Rv1986 may be a special region that undergo antigenic variation in response to host immune pressure and may be involved in ongoing immune evasion. The dN/dS value of all six genes (including MPT64) were 2.33, much higher than 1, which means T cell antigens in RD2 region appeared to be under diversifying selection. Our data support the view that RD2 regions tend to be more variable than we expected to evade host immunity and the immune-related antigens in RD2 were more variable than we expected, especially in T-cell epitope regions.