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In this data article, we provide the scientific and theoretical data on fish taxonomy including class, order, family, and genus in the Yangtze River. The Yangtze basin is divided into 56 units, and their geological information including latitude, longitude, latitude, and channel length is recorded. Fish presence/absence data at the unit scale are reported. Biological traits including morphological, physiological, and ecological characters of each fish species are also described, numeralized, and reported. These data are the foundation of the analyses and results in the article “Continental-scale analysis of taxonomic and functional fish diversity in the Yangtze River” (Kang et al., 2018).