Hucho taimen and Hucho bleekeri belong to Salmoniformes, Salmonidae. Hucho are a genus of ferocious large cold-water fishes. There are two main distribution areas of H. taimen in China, namely, the Heilongjiang River Basin in the northeast and the Irtysh River Basin in the northwest. Existing research shows that from the early to the middle of the tertiary period, the Heilongjiang River Basin and the Irtysh River Basin were connected by a vast lake group distributed in northern China and Mongolia. Based on this geographical condition, the H. taimen in the two basins could freely communicate and diffuse in this period. After the middle of the tertiary period, the rivers and lakes connecting the Heilongjiang River Basin and the Irtysh River Basin shrank, and the gene exchange between the two basins stopped as the two basins became geographically isolated. H. bleekeri is an endemic species in China and the species with the lowest distribution latitude among the five species of Hucho. During the quaternary glacial period, the climate of Sichuan Province, Shaanxi Province, and Qinghai Province became cold, and H. bleekeri ancestors moved south from the northern region with a high latitude to the Yangtze River Basin. After the end of the ice sealing period, they stayed in the rivers with high altitudes and low water temperatures, and gradually evolved into the existing H. bleekeri, which is considered as a living fossil for studying the relationship between fish evolution and climate change. To determine the internal and external morphological variation between the rare and endangered H. taimen and H. bleekeri, H. taimen from Xinjiang Uygur Autonomous Region and Heilongjiang Province and H. bleekeri from Shaanxi Province were used as the research object. Nine segmented characteristics and 35 standardized measurement characteristics of the three populations were statistically analyzed using the traditional morphological method and the frame measurement method. The results showed that there was a significant difference in the mean number of lateral line scale between the two geographical populations of H. taimen (P＜0.05), but as a whole, the two populations of H. taimen had individual crossover in all nine segmented characteristics, which could not be distinguished. The average number of dorsal fin branched fin-ray, lateral line scale, and pyloric caecum of H. bleekeri was significantly lower than that of H. taimen (P＜0.05), and there was no individual crossover between these three parameters, so the distinction was obvious. Four principal components with eigenvalues greater than 1 were screened out using principal component analysis, with a cumulative contribution rate of 88.928%, of which the first principal component had the highest contribution rate, which mainly explained the difference in trunk oblique morphology of the three groups. Constructing the two-dimensional scatter plot of principal components, it was found that although the three groups can form relatively independent groups, there were still individual intersections among them, which indicated that the difference in measurement characteristics of the three groups couldn’t be described simply by any two principal components, and all principal components should be considered comprehensively. One-way ANOVA showed that there were only 14 significant differences (P＜0.05) in the measurement characteristics mainly describing the head and tail of H. taimen, while there were 29 significant differences (P＜0.05) in the measurement characteristics mainly describing the trunk between H. taimen and H. bleekeri. A total of 10 measurement characteristics were screened out by discriminant analysis to establish Fisher linear discriminant function, and the discriminant rate of individuals being correctly classified into their respective populations was as high as 100%. Cluster analysis showed that the two geographical groups of H. taimen had the closest genetic relationship, and the genetic relationship between H. bleekeri and the H. taimen from the Xinjiang Uygur Autonomous Region was closer than that of Heilongjiang Province. The comprehensive analysis shows that: (1) there were some morphological differences between the two geographical groups of H. taimen, but they still belong to the same species; and (2) the morphological variations between H. taimen and H. bleekeri were concentrated in the trunk. The segmented characteristics such as the dorsal fin branched fin-ray, lateral line scale, and pyloric caecum could be used as the identification characteristics of the two species. H. bleekeri might have evolved from H. taimen from the Xinjiang Uygur Autonomous Region.