Abstract: Gymnocypris eckloni is widely distributed in the Yellow River and Qaidam River in the northeast of the Qinghai-Tibet Plateau, China. Inconsistence between morphology and phylogenetics was observed in two different drainage G. eckloni. On this basis, we speculated that the first was the morphological convergence caused by the similar ecological pressure of the two water systems, and the second was the traditional measurement method, which makes some subtle morphological features undiscovered. Hence, the combination of geometric morphometrics and Micro CT revealed the phenotypic difference among G. eckloni of two water systems. The structure of G. eckloni’s head was almost identical between two drainages, demonstrating a significant difference in their bone structure. The divergence between head morphology and molecular data were presumably attributed to one reason. It may be that the morphological convergence caused by the similar ecological environment of the two river systems misled the taxonomic status of Gymnocypris eckloni of two water systems. The current study has laid a morphology foundation for correctly evaluating the real relationship between Gymnocypris eckloni of two water systems, and suggest that bone is an accurate standard for taxonomic classification in schizothoracin fishes. More molecular markers are required for further research to uncover the evolutionary pattern of G. eckloni from different geographic distribution.