Abstract: Schizopygopsis stoliczkai, belongs to family Cyprinidae, distributes in the lakes and rivers in Qinghai-Tibetan Plateau, China. The morphological differences in the species are attributed to the local environments, hence identifying the variations helps to improve our understanding of micro-evolution theory and provide the guidance for the ecological and biodiversity protection. To explore the morphological diversity, we quantitatively measured the cephalic contour in Schizopygopsis stoliczkai from five different geographical populations using modern geometric morphometrics. The principal component analysis (PCA) and canonical variate analysis (CVA) revealed that the varia-tions among five geographical populations were mostly in the shapes of the lower part rhynchodaenm, orifice of mouth, mandible and sharp clogs. Furthermore, PCA, CVA and cluster analysis showed that the three subspecies of S. stoliczkai stoliczkai, S. stoliczkai maphamyumensis and the S. stoliczkai bangongensis were separated. The samples from each subspecies were clearly grouped together based on PC1, which strongly supported the reliability of three subspecies in S. stoliczkai. The Procrustes distance and the Mahalanobis distance suggested that five geographical populations could divide into two categories:the lacustrine type and the riverine type, which supported by cluster analysis. Taken together, we profiled the morphological variations in the head of S. stoliczkai, and classified the fish into two types, which might regulate by natural resources and environment of lake and river.