Schizothoracinae species are the largest group of Cypriniformes that readily adapt to the natural conditions of the Qinghai-Tibet Plateau. This group has habitat characteristics and distribution patterns centered on the Qinghai-Tibet Plateau. To study the evolution of three Schizothoracinae species in Northwest China, the evolutionary characteristics of these species were explored based on differences in otolith morphology and skeletal morphology. From 2020 to 2022, 138 samples (63 Aspiorhynchus laticeps, 35 Diptychus maculatus and 40 Schizothorax pseudaksaiensis) were collected from the Tarim River and Ili River, 6 basic morphological parameters of otoliths were measured and converted into 6 morphological factors and 7 morphological indices. A total of 77 Fourier transform coefficients of each otolith were selected The first three principal components accounted for 92.834% of the total variation in 13 otolith morphological indices of the three Schizothoracinae species, and the overall discrimination rate was 94.20%. According to the principal component analysis of 77 Fourier harmonic values of otoliths, the first 20 principal components explained 97.233% of the total variation, and the overall discrimination rate was 100%. The results of the cluster analysis directly reflected the relationships between related species. The differences in the bone morphology of the three Schizothoracinae species were particularly reflected in the number of whiskers, pharyngeal teeth and vertebrae, and there were also significant differences in the shapes of the sphenotic (SP), pterotic (PTE), preoperculum (PO), branchiostegal ray (BRA) and basibranchial (BB) bones. Their unique morphological and skeletal characteristics are closely related to geological changes and water system evolutionary trends. This study contributes to the understanding of species identification and the evolutionary status of plateau fishes, provides a reference for further evolutionary classification and for assessing the evolutionary mechanisms of plateau fishes, and provides a scientific basis for phylogeny and germplasm resource protection.

The genus Schizothorax comprises an important group of freshwater fishes in Xinjiang (China); however, detailed information on their skeletal anatomy remains limited. In this study, we combined micro-computed tomography (micro-CT) and traditional skeletal preparations to examine and compare the osteological characteristics of three representative Schizothorax species: Schizothorax biddulphi, Schizothorax eurystomus, and Schizothorax curvifrons. Distinct variations were observed in several skeletal structures, including the cranium, pharyngeal teeth, fin-supporting elements, and vertebrae. Among the three species, S. biddulphi and S. eurystomus showed generally similar skeletal architectures, whereas S. curvifrons exhibited more pronounced osteological differences. These findings provide new comparative osteological data for Schizothorax species and offer a morphological reference for future studies on the taxonomy, systematics, and conservation of these freshwater fishes.