Abstract: Hucho taimen belong to endangered species. It is distributed in the Irtysh River basin and the Heilongjiang River basin, but the geographic isolation has existed between two basins chronically. Differences in the morphology and anatomy of Hucho in the two basins have been reported, yet the differences in gene sequences remain unclear. Several Hucho were collected from natural waters (Hucho BHB and Hucho BEJ), and introduced from Heilongjiang (Hucho HLJ). The morphological characteristics were described. The COⅠ gene was amplified and sequenced, and the phylogenetic tree was constructed by downloading the COⅠgenes from GenBank. The results indicated that Hucho BEJ and Hucho HLJ had the same morphological characteristics, and Hucho BHB differed from the other two species on body color and spot size. The phylogenetic tree based on the COⅠgene showed that the three different Hucho and H. taimen were clustered into one large branch, and that Hucho BEJ, Hucho HLJ and Russia’s Amur River (called the Heilongjiang River in China) were gathered into a common group, and Hucho BHB was another separate group. Based on the genetic matrix of the COⅠgene, Hucho BEJ and Hucho HLJ had similar genetic distance with the Russian Amur River (0—0.0044), and Hucho BHB was far away from Hucho BEJ, Hucho HLJ and Hucho of Russian Amur River (called the Heilong River in China) (0.0057—0.0082). These results indicated that Hucho BHB in morphology and gene sequence is quite different from Hucho HLJ and Russia’s Amur River (called the Heilongjiang River in China), which maybe belong to different ecological and geographical types. The almost identical morphology and gene sequence between Hucho BEJ and Hucho HLJ demonstrated that Hucho BEJ was a species released into the river or escaped from the farm.