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Species coexistence is one of the most important concepts in ecology for understanding how biodiversity is shaped and changed. In this study, we investigated the mechanism by which two small cyprinid fishes (<i>H. leucisculus</i> and <i>H. bleekeri</i>) coexist by analyzing their niche segregation and morphological differences in the upper Yangtze River. Morphological analysis indicated that <i>H. leucisculus</i> has posteriorly located dorsal fins, whereas <i>H. bleekeri</i> has a more slender body, bigger eyes, longer anal fin base, and a higher head. Niche segregation analysis showed spatial and trophic niche segregation between these two species: on the spatial scale, <i>H. leucisculus</i> was more widely distributed than <i>H. bleekeri</i>, indicating that <i>H. leucisculus</i> is more of a generalist in the spatial dimension; on the trophic scale, <i>H. bleekeri</i> had a wider niche than <i>H. leucisculus</i>. Therefore, these two species adopt different adaptation mechanisms to coexist