Objective To study the genetic variation among Schistosoma japonicum from the mainland of China through the microsatellite investigation. Methods S.japonicum isolates were obtained from seven endemic provinces across the mainland of the People's Republic of China: Zhejiang (Jiashan), Anhui (Guichi), Jiangxi (Yongxiu), Hubei (Wuhan), Hunan (Yueyang), Sichuan (Maoshan,Tianquan), Yunnan (Dali), and also Sorsogon Province, the Philippines. DNAs from 20 individuals from each origin were screened against six recently isolated and characterized S.japonicum microsatellites, M5A, J5N, MF1, RRPS, 2AAA and MPA, which were selected based on their polymorphic information content. Results High levels of polymorphism were found between and within population samples, with Chinese and Philippine strains appearing to follow different lineages, and with distinct branching between the provinces. Moreover, across the mainland of China, genotype clustering appeared to be related to the habitat type and/or intermediate host morphology. Conclusion These results demonstrate the suitability of microsatellites for population genetic studies of S. japonicum and suggest that there may be different strains of S. japonicum in the mainland of China.