In order to research the genetic diversity of different populations of Paramisgurnus dabryanus, four populations from Liaoning, Henan, Hubei and Taiwan were analyzed by sequencing the mitochondrial cytochrome oxidase subunit Ⅰ(COⅠ) genes. The results showed that 642 base pairs (bp) fragments was consisted of A, T, C and G base with 23.5%, 30.6%, 26.7% and 19.2%, respectively, indicating a preference for A and T bases. A total of 44 mutations of nucleotide and 23 haplotypes were identified in 4 populations. The haplotype diversity index ranged from 0.424-0.855, and the nucleotide diversity ranged from 0.000 84-0.016 59. The results indicated that Paramisgurnus dabryanus from Taiwan population had a higher genetic diversity than Liaoning, Henan and Hubei populations. The genetic differentiation index (Fst) and genetic distance showed that genetic differentiation between Taiwan and other populations represents extremely significant difference, also had a further genetic distance with other populations. In general, the results showed that there was a certain genetic difference between the different geographical groups, AMOVA analysis revealed that 52.11% of genetic variations derived among populations and 47.89% of genetic variations occurred within populations. In terms of the negatively selective neutrality test, the results indicated that a population expansion occurred in the populations of Liaoning, Henan and Hubei population, and provided a reference for protection of the genetic diversity and breeding work of Paramisgurnus dabryanus.