<p>The longfin barb (<i>Acrossocheilus longipinnis</i>) is a rare fish and an economically important species native to the Hongshui River in China. In recent years, wild populations of <i>A. longipinnis</i> have shown a significant decline, leading to its classification as a vulnerable species. However, the lack of genomic resources has hindered conservation efforts and breeding research for this species. In this study, we generated two high-quality, haplotype-resolved genome assemblies for a male <i>A. longipinnis</i> using PacBio HiFi, ONT ultra-long and Hi-C data. The resulting assemblies, designated as hap1 and hap2, span 922.22 Mb and 920.68 Mb, with Contig N50 values of 36.45 Mb and 34.89 Mb, respectively. Both haplotype assemblies were anchored to 25 chromosomes, and complete centromeric regions were resolved for 25 chromosomes in hap1 and 24 chromosomes in hap2. Completeness assessment using BUSCO revealed high genome integrity scores of 98.9% for hap1 and 98.4% for hap2. Genome annotation predicted 30,424 and 30,441 protein-coding genes in hap1 and hap2, respectively, with 96.94% and 96.74% of these genes being functionally annotated. Additionally, repetitive elements were identified to comprise 56.20% and 56.52% of the total genomic content. These high-quality genome assemblies provide invaluable resources for the conservation, molecular breeding, and evolutionary studies of <i>A. longipinnis</i>.</p>