To analyze the morphometric differentiation of wild between the population from the Yangtze River Basin and that from the Pearl River Basin, the variation in morphological characteristics of among three populations from three different sampling sections (Yanhe section of the Wujiang River, Tongren section of the Jinjiang River in the Yangtze River Basin, and Guanling section of the Beipanjiang River in the Pearl River Basin) were assessed using multivariate analysis methods based on the measured morphological data and the truss network. The results showed that among the three populations, the eyes of the individuals from the Tongren section were the smallest, the body width from the Yanhe section was the thinnest, and the population from the Guanling section had the thickest body width, the shortest snout length, but the longest caudal peduncle length. After standardization and parameter selection for original data, the data for 12 selected characters were used to conduct principal component analysis. Two principal components were constructed, which resulted in a cumulative contributory ratio of 64.255%. Principal component 1 was mainly affected by characters, including body width, caudal peduncle shape, and distance between the eyes, whereas principal component 2 was mainly affected by the length of the snout and size of the eyes. A stepwise discriminant method was used to establish the characteristic discriminant functions of the three stocks, which revealed that the total accuracy rate of discrimination by the cross-validated method was 91.85%. The coefficients of differences for the 12 characters among the three stocks did not reach the threshold value of 1.28, although the subspecies could be clearly discriminated. In short, the morphometric differentiation between the two populations from the Yanhe section and Tongren section in the Yangtze River Basin were low, whereas the morphological differences were higher between these two populations and the population from the Guanling section sampled from the Pearl River Basin. Nevertheless, the morphological variation of the three populations shown in this study represented morphological variation from different geographic populations of the same species, which had not reached the level of subspecies variation.