Objective The genetic and evolutionary variation of different Opsariichthys bidens poputions were explored, which would provide a theoretical basis for the further protection and the maintenance of genetic diversity of breeding populations.

Methods In this study, 136 O. bidens individuals were collected from Mudanjiang River (MDJ), Futunxi River (FTX), Jianxi River (JX), Tingjiang River (TJ) and Nandujiang River (NDJ). The mitochondrial DNA (mtDNA) Cyt b gene and D-loop region sequences from each individual were identified and analyzed.

Results The results showed that the total haplotypes defined by Cyt b gene and D-loop region in all populations were 35 and 37, respectively; the corresponding overall haplotype diversity (H_d) and nucleotide diversity (π) were 0.922 and 0.05426 (Cyt b), and 0.875 and 0.028 24 (D-loop), respectively. The data based on Cyt b gene and D-loop region showed that the genetic diversity of the TJ population was higher than those of the other four populations, and the MDJ population was lower than other populations. The genetic distances among the population were 0.00304−0.10311 (Cyt b) and 0.00089−0.05153 (D-loop). The analysis of molecular variance (AMOVA) indicated that the source of variation between populations 96.00%（Cyt b)、62.23%（D-loop） was significantly higher than that within populations 4.00%（Cyt b)、37.77%（D-loop）. This suggests a substantial genetic differentiation among these populations (P<0.05). Phylogenetic tree constructed by the maximum likelihood (ML) method based on Cyt b gene showed that five O. bidens populations could be divided into three branches: one branch was clustered with the haplotypes collected from JX, FTX and Jiulong River population, the second branch was clustered with the haplotypes collected from MDJ, Amur River, Tumen River and Liao River population, while NDJ population and Hainan population were clustered into the third branch. A neutral test and mismatch distribution analysis suggested that O. bidens collected from FTX, JX, TJ and MDJ had no undergone a recent population expansion, and which collected from NDJ had undergone a recent population expansion perhaps.

Conclusion Overall, obvious genetic differentiation among the five populations were observed with the NDJ and TJ population having the higher genetic diversity, but MDJ, FTX and JX population having the lower genetic diversity. The results could provide scientific evidence for the conservation, sustainable development, and commercial utilization of germplasm resources of O. bidens.