The schizothoracinae fishes are mainly distributed in the Qinghai-Tibetan plateau and its adjacent regions, most of which turn into important commercial fishery resources in southwest of China. As the wild population decreased quickly, the research of basic biology becomes essential, especially the interspecific morphological classification, which offers scientific data for the fish conservation and utilization. The interspecific and intraspecific morphological variations of 89 specimens from Kozlov's Schizothoracin (Schizothorax kozlovi) in Wujiang River and 33 specimens of David's Schizothoracin (S. Davidi) in Minjiang River were analyzed by three multivariate analysis methods based on 10 traditional morphological parameters and 20 truss network features. The methods of hierarchical cluster analysis consisted of Euclidean distance and between-groups linkage, and the plots of dendrogram showed highest similarity of S. kozlovi from three collections and contrasted with the lowest of S. Davidi (Fig. 2). In principal component analysis of covariance matrix, 8 principal components were extracted with the cumulative contribution rate of the total variance of 72.762%, and the most contributions of characters were focused on snout and posterior torso (Tab. 3). Based on two steps of discriminant analysis by the method of Wilks’ lambda, 122 specimens were finally divided into two groups and the total discriminant accuracy reached 100% (Fig. 4). All results suggested that two fishes were significantly different from each other, and the distinct differences were snout and posterior torso. The samples of S. kozlovi were from the same population, and S. kozlovi and S. davidi could be identified by the three multivariate analysis methods.