Onychostoma macrolepis is an emerging commercial fish with high edible value. Due to overfishing and environmental pollution, the wild population of Onychostoma macrolepis is declining sharply. In this study, we successfully assembled a chromosome-level genome for Onychostoma macrolepis using a comprehensive approach that integrated Illumina sequencing, PacBio sequencing, and Hi-C technology. The genome spans is 944.02 MB, the contig N50 is 32.36 Mb, 99.15% of the assembled sequences are anchored on 25 chromosomes. A total of 26,294 protein-coding genes were predicted, among which 96.30% were functionally annotated. The high-quality genome data of O. macrolepis obtained in this study provide reliable resources for further research and restoration of wild germplasm resources.