[Objectives] The Siberian Flying Squirrel Pteromys volans is an arboreal, nocturnal, and gliding rodent. It plays an important role in the dispersal of forest seeds and the maintenance of ecosystem balance. In northeast China, the population and distribution of the Siberian Flying Squirrels are decreasing due to deforestation and habitat loss. As an important indicator species for sustainable forest management, it has been listed in the Catalog of Terrestrial wildlife Species with Significant Ecological, Scientific, and Social Value in China. It has also been listed as “Vulnerable (VU)” in the Red List of China’s Vertebrate. There is an urgent need to further evaluate genetic changes of the population, especially genetic diversity and gene flow, to enhance the pertinence of conservation and management. [Methods] From 2018 to 2023, we collected hair samples from 20, 26, 15 and 27 Siberian Flying Squirrel individuals from four geographical populations (Fangzheng, Bin County, Weihe and Muling) in southern Heilongjiang Province, northeast China, respectively (Fig. 1 and Table 1), and evaluated their genetic diversity and structure based on the complete sequences of mtDNA control region (1 070 bp). [Results] The results showed that 155 variation sites and 67 haplotypes were detected in the control region sequence of these 88 individuals. In the populations, the haplotype diversity (H_d) and nucleotide diversity (P_i) were 0.992 (0.945﹣0.986) and 1.772% (1.221%﹣1.974%), respectively (Table 2). Only one haplotype (H_20) was shared by two populations (Bin County and Weihe), and there were 52 haplotypes with only one individual, and the proportion of rare haplotypes is 77.16% (52/67) (Figs. 2 and 3). The genetic differentiation coefficient (F_ST) and gene flow (N_m) between populations were 0.051 3﹣0.135 7 (P < 0.05) and 3.19﹣9.24, respectively (Tables 3﹣5). The Mantel test indicated that genetic and geographic distances were not significantly positively correlated (r = 0.413, P > 0.05). [Conclusion] Thegenetic diversity of the populations was at a high level, among which the Weihe and Muling populations were the highest, followed by the Bin County population, and the Fangzheng population was the lowest. This may suggest that the Changbai Mountains were the refuge for Siberian Flying Squirrels during the last glacial period. However, the high proportion of rare haplotypes indicated a risk of declining genetic diversity of the Siberian Flying Squirrel population in the future. There were significant moderate levels of genetic differentiation among the four populations, and the distance isolation model could not effectively explain the current population genetic pattern. The phylogenetic tree constructed by maximum likelihood, Bayesian inference method and haplotype network indicated that there was no obvious phylogeographic separation among the four geographic populations (Figs. 2 and 3). This result implies that the geographical barriers between the populations may be recent. It is suggested that conservation efforts for the Siberian Flying Squirrels should be improved, and that habitat restoration and ecological corridor construction should be carried out in the field, to improve gene exchange between individuals and accelerate population restoration.