Background To study differences among Paragonimus skrjabini ( P. skrjabini) populations from five provinces in China (Guangdong, Fujian, Yunnan, Hubei, and Sichuan ) and Paragonimus szechuanensis.Methods DNA sequences were obtained from the ITS2 and CO1 genes and phylogenetic trees were constructed from the results. Sequences were also obtained from several other species of Paragonimus for comparative purposes.Results Although differences existed in the DNA sequence among P. skrjabini populations from five provinces, the differences were very small. There was also some resemblance between P. miyazakil from Japan and Fujian strains of P. skrjabini.Conclusion All studied populations can be regarded as different strains of P.skrjabini; P.szechuanensis is not a separate species but may be a geographical strain of P. skrjabini. We also found that P.iyazakii may be synonymous with P. skrjabini.