Sequences of mitochondrial COI gene of 71 individuals of Yangtze River, Liao River, Ou River population and F₁ generation of Rhine River population were determined. The result showed that there were 112 variable sites population and 36 parsimony-informative sites in total 628 sites. The content of (G+C) was lower, showing obvious bias of base composition. Seventeen haplotypes were detected among the 71 samples. Haplotype H13 which occurred most frequently was shared by the populations from Yangtze River, Ou River, and F₁ generation of Rhine River population. Haplotypes H15, H16 and H17 were unique in the population from Ou River. Haplotype diversity index () was 0.016 9 indicating that the genetic diversity index of total samples was high. Yangtze River population had the highest (0.838) while the F₁ generation of Rhine River population had the lowest (0.725 0) haplotype diversity index among the four populations. The genetic distance between Yangtze River population and Liao River population was closer than that among others and it can be inferred that the genetic exchange between them was more frequently. The genetic distance within Yangtze River population (0.017 38) was higher than those of others except of Ou River population which indicating that higher genetic variation and more serious genetic admixture exist within Ou River population. Gene flows () among four populations were all above 1, especially between Yangtze River population and Liao River population (8.27) and between Yangtze River and F₁ generation of Rhine River (9.72), respectively, which indicated that the population of Yangtze River had frequent gene flow with the other two before. Analysis of molecular variance (AMOVA) showed that genetic differentiation index of all the four populations was 0.2685 (P<0.001), of which the majority (90.77%) existed within populations, and the rest existed among populations (9.23%). Haplotype network diagram and phylogenetic analysis did not show any correlation between haplotypes and geographical location, suggesting that currently there exists genetic admixture of in the four water systems, and the four populations could not form distinct geographic group structures.