Schistosoma japonicum in China has been one of the most serious public problems. Subspecies of the pomatiopsid snail species Oncomelania hupensis is well known as the intermediate S. japonicum host. We used the simple sequence repeat anchored PCR (SSR-PCR) to assess the systematic position of the snail populations from the northwestern part of Guangxi Province, and to assess the degree to which SSR-PCR derived relationships are congruent with the allozymes, COI, and AFLPs results. For 19 populations studied, the genetic distance D ranged from 0.00 to 0.73, with an average value 0.22 ± 0.013. The cophenetic correlation coefficient for the Complete-link cluster, Single-link cluster, UPGMA cluster and NJ cluster was 0.932, 0.906, 0.939 and 0.733, respectively. The goodness of fit for these clusters except NJ cluster was very good. These results were very similar to the results of the AFLPs analysis data. The patterns of genetic differentiation are basically consistent with geographic distribution and shell sculptural and shape characters. These patterns thus serve as the basis for subdivision of O. hupensis into four discrete subspecies, O. h. hupensis (Gredler, 1881), O. h. robertsoni (Bartsch, 1946), O. h. tangi (Bartsch, 1936), and O. h. guangxiensis (Liu, 1981).