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Ancherythroculter nigrocauda is a cyprinid fish endemic of the Upper Reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. On the other hand, A. nigrocauda is a threatened species as a result of overfishing, dam construction, and water pollution. In this study, a chromosome-level genome assembly of A. nigrocauda is reported and built using PacBio sequencing and the Hi-C technology. The 1.04 Gb sequenced genome of A. nigrocauda contained 2,403 contigs, with an N50 length of 3.12 Mb. Then, 1,