Taimen (Hucho taimen) is an important local wild commercial fishery species in Heilongjiang River. Due to severe damages to its population size, habitats, and spawning fields from overexploitation and environmental pollution. It is enlisted as an endangered species in the “China Red Data Book (Pisces)”. To establish a scientific basis to conserve taimen, studies on the population genetic structure and phylogeography are necessary. In this paper, a total of 30 individuals, a selection from nine geographic areas along Heilongjiang River, were analyzed for genetic variances in their mitochondrial Cox1 (1550 bp) and ND1 (1000 bp) gene sequences. The sequence information identified 10 haplotypes in the Cox1 gene. The average sequence divergence (Da) between individuals was 0.0013, while it was 0-0.0022 within a population and 0-0.0028 between populations. Seven haplotypes of ND1were also identified in this study. The average sequence divergence (Da) between individuals was 0.0006, while the range within a population and between populations were both 0-0.0013. Fst values were 0.0704, 0.0491, and 0.0792 for Cox1, ND1, and the combination of both genes. These data showed significant genetic variances (P<0.05) among geographic populations. The taimen populations in Heilongjiang River could be divided into four subpopulations based on Fst values between these geographic populations. However, these populations shared one common haplotype (BH11) shown by haplotype network (TCS) and haplotype distribution frequency analysis. This suggested that they evolved from a common ancestor (likely a population in the upstream of the Heilongjiang river) and shared common gene flows.