Within and among populations genetic variance of twelve Hemarthria compressa populations and one Hemarthria japonica population from China were analyzed using inter simple sequence repeat (ISSR). Twelve primers amplified a total of 165 genomic DNA fragments across a total of 148 individuals of which 156 were polymorphic (94.55%). 75.76% of the bands were unique to each species, while the average genetic distance (GD) between one population of H. japonica and twelve populations of H. compressa was 0.44, which suggest that there was distinct differentiation between these two species. In H. compressa, twelve primers produced 145 bands across 145 individuals. High genetic diversity was observed at species level. The percentage of polymorphic loci (P) was 86.21% and Shannon's information index of diversity (I) was 0.357. In contrast, there were relatively low levels of genetic diversity within population (P=32.93%, I=0.174). Analysis of molecular variance (AMOVA) showed that a considerable proportion of genetic variation (48.02%) resided among populations. The coefficient of gene differentiation (G(ST)=48.6%) also suggested that there was strong genetic differentiation among H. compressa populations in southern China. An indirect estimate of the number of migrants per generation (N(m)=0.264) indicated that gene flow was low among populations of this species. Relative high clonal diversity was found, and all local genotypes were found.