Objective In order to discover the superiority of Chinese two-end-black pigs in Xenotransplantation, this study used DNA and RNA methods to identify gag, pol and env genes of PERV in five Chinese two-end-black pig breeds (Tongcheng pig, Dongshan pig, Ganxi two-end-black pig, Shaziling pig and Jinhua pig) and three western breeds (Yorkshire, Landrace and Duroc). Methods Detected the existence of gag, pol and env-A, B, and C genes of PERV by PCR, and the expression level of gag, pol and env gene of PERV in nine tissues of Tongcheng and Yorkshire pigs by semi-quantitative RT-PCR. Results In four two-end-black pigs of central China, env-AB gene subtybe was the major subtype of PERV, whose positive rates were from 92% to 100%. Env-C gene subtype wasn’t identified in all these four breeds, but was in Jinhua and western breeds. Gag and pol genes expressed in nine tissues of all. In Tongcheng pigs, expressions of env-A in heart, liver, lungs, adipose and lymph were much lower than other tissues, while the expressions of env-B were much lower in heart and lymph. In Yorkshire, env-A was equally expressed in all nine tissues while expression of env-B was lower in kidney. Conclusions The results indicate that four two-end-black pigs of central China have great potential value in xenotransplantation.