Abstract: 【Objective】 Comparative study on morphological and skeletal differences of two Schizothorax species in Tarim River system. The provide scientific reference for the systematic evolution and geographical distribution pattern of the plateau fish. 【Methods】 To study the external morphology and skeletal system of Schizothorax irregularis and Diptychus maculatus which are endemic to Xinjiang by anatomical comparison. Principal component analysis of morphological features was carried out by combining frame data and traditional quantifiable data and then the difference of bone morphology between CT scanning and boiling cutting was compared. 【Results】 Among 31 proportional traits of Schizothorax species, there were significant differences in 1-2/ body length (BL) (P< 0.05), body width (BW/BL) and other 25 proportional traits were significantly different (P< 0.01); In the principal component analysis, the cumulative contribution rate of the first two principal components was 56.74%, and the difference was mainly reflected in the body head and the front torso. The number of cranial, pharyngeal and appendicular bones of the two Schizothorax species was the same, with 42, 80 and 132, respectively. However, there were some differences in the number of vertebrae and ribs between the two Schizothorax species: there were 4+42-43+1 vertebrae and 20-21 ribs in S. irregularis(2 tails), and there were 4+34-35+1 spines and 17-18 ribs in D. maculatus(2 tails). On some bones, such as the 2nd preethmoid, sphenotic, pterotic, premaxilla, maxilla, pterygoid and mstapterygoid, especially in the pharyngeal, the differences between the two Schizothorax species were more pronounced. 【Conclusion】 The morphological and skeletal differences of the two Schizothorax species in the Tarim River system are obvious, and their evolutionary mechanisms are closely related to the uplift of the Qinghai-Tibet Plateau. The unique morphological and evolutionary characteristics and skeletal differences can be further served as the basis for the classification and identification of fish, which might enrich the biological data of their morphological and evolutionary evolution.