The genetic divergence between geographically separated populations can be studied by comparing the divergences in their allele frequencies to the geographical distance of popula-tions. The present study is to examine the divergences in allele frequencies and genetic diver-gence in relation to the geogrephical distance of the samples localities, in order to test the population structure model of Oncomelania from the endemic areas in mainland China.The results showed that three patterns of allele frequency distributions occured in seven polymorphic loci, which were even,chaotic and discontinuous cline distributions. The distcon-tinuous or stepped clines shown in loci Est-4,Got and Mdh-2 suggested that the discrete subpopuation model is the likeliest. The plot of genetic distance (Nei's 1978) between sample populations against the geographic distances suggested that the special pattern of allele fre-quency distribution could be found. The regression analysis shows that logistic sigmoid re-gression is the best model to fit the original data in the plot. This supports the existence of the discrete subpopulations model in the population structure studied.