To correctly determine the genetic structure of wild populations from Haihe, Yellow, Huaihe, and Yangtze River basins in Henan Province, we analyzed the population genetic diversity and differentiation of the species using mitochondrial CO I gene. A total of 110 individuals were sequenced, which have defined 40 distinct haplotypes. The average haplotype diversity and nucleotide diversity were 0.92077 and 0.02439, respectively. Analysis of molecular variance (AMOVA) indicated that most of the genetic variation existing among populations (60.59%), and the remaining 37.67% of genetic variation was attributed to differentiation within populations. The assignment of populations based on Neighbor-Joining (NJ) method revealed that populations from Yangtze River divided into two distinct mitochondrial DNA lineages, one clustered from the ZY population and the other clustered individuals from Haihe River, Yellow River and Huaihe River. This phylogenetic pattern is not consistent with the previous reported North and South Clades. Demographical history analysis indicated that populations had undergone a bottleneck which coincided with the middle Pleistocene and suffered from climate changes. Considering the genetic and phylogeographic results obtained in this study, appropriate measures are proposed to conserve population, especially for those with low genetic diversity in Haihe River basin.