Hemibarbus maculatus, a keystone cyprinid species widely distributed across Asian freshwater ecosystems, holds dual significance as an economically valuable food fish and an ecological regulator. However, research on H. maculatus predominantly prioritizes nutritional profiling, aquaculture technology, and ecological traits, neglecting developmental molecular mechanisms and genomic markers, while taxonomic and evolutionary studies rely heavily on mitochondrial data and are hindered by the lack of a high-quality genome and short-read sequencing limitations in resolving its heterozygous wild population genomes. Here we present its first chromosome-level genome assembly by integrating PacBio HiFi reads and Hi-C scaffolding. The 1.08 Gb assembly achieves exceptional continuity with a contig N50 of 43.84 Mb, where 98.23% sequences are anchored to 25 pseudochromosomes. BUSCO assessment confirmed 99.1% completeness, with 30.02% repetitive elements and 23,892 predicted protein-coding genes