The Pearl River Basin, as the largest river of southern China, comprises the Xijiang River, North River, East River and Pearl River Delta. With abundant water and fish resources, Xijiang River, which comprises the Nanpan River, Hongshui River, Qianjiang River, Youjiang River and Zuojiang River, has a wide basin that represents 77.8% of the Pearl River Basin. The big-eye mandarin fish (i Garman, 1912), belonging to the Perciformes, Serranidae, , is a special and precious freshwater fish distributed only in China, especially in the Pearl River. , which is a carnivorous freshwater fish with a favorable taste and abundant nutrients, has become one of the most important commercial freshwater fish in China, and has the potential to be a candidate aquaculture species because of its significant economic and ecological value. However, some negative factors, such as the constant severe water pollution, the building of water conservation engineering works, overfishing, and electrifying and bombing of fishes, have led to its miniaturization, low annualized phenomenon and rapid reduction of its wild population. Morphological differentiation among three wild populations (YJ:Youjiang River, ZJ:Zuojiang, HSH:Hong Shui He River) of in the Pearl River was studied based on traditional morphology and a truss network of distance measurements. We aimed to learn more about the germplasm resource of by determining the differences among the three populations and to provide reliable scientific evidence to underpin the protection and use of germplasm resources of . Three multivariate analysis methods were used (One-Way ANOVA, principal component analysis and cluster analysis) for 33 morphometric proportional parameters, using SPSS17.0 software. Based on the LSD results of one-way ANOVA for the measurable characters, there were significant differences between three populations, mainly in the head and tail traits. Specifically, there was a significant difference in the head traits[HW/BL, ED/BL, U (10-11)] and tail traits[CPL/BL, N (5-6)] between the HSH population and ZJ population, and between the HSH population and YJ population, respectively; however, there was no significant difference between the ZJ population and YJ population. For the morphological differences among populations, the contribution of the truss network of distance measurements C(1-11), E(2-11), F(2-10), G(3-4), I(3-9), M(4-10), K(4-9), J(4-5), T(9-10), O(5-8), N(5-6), P(5-7), R(7-8) and S(8-9) indicated that the truss network of the head and trunk of was the principal component, and the contribution of traditional characters was the second. Cluster analyses suggested consistently that the ZJ and YJ populations clustered first and then clustered with the HSH population, whether based on the traditional morphology or the truss network. All of the above indicated that morphological differentiation nexisted among the three populations and was closely associated their geographical distribution. The results, representing basic knowledge of in Pearl River, provide reliable scientific evidence for the protection and use of germplasm resources and for artificial selection breeding of .