Abstract: Hapalogenys analis (order Lobotiformes) is an economically and ecologically significant fish species. It is a typical sedentary rocky reef fish and is primarily found in the northern Pacific Ocean. Here, we used Hi-C and PacBio sequencing technique to assemble a high-quality, chromosome-level genome for this species. The 539 Mb genome had a contig N50 with a size of 3.43 Mb, while 755 contigs clustered into 24 chromosomal groups with an anchoring rate of 99.02%. Of the total genomic sequence, 132.74 Mb (24.39%) were annotated as repeat elements. A total of 21360 protein-coding genes were identified, of which 20787 genes (97.32%) were successfully annotated to public databases. The BUSCO evaluation indicated that 96.90% of the total orthologous genes were matched. The phylogenetic tree representing H. analis and 14 other bony fish species indicated that the H. analis genome contained 364 expanded gene families related to olfactory receptor activity, compared with the common ancestor of H. analis and Sciaenidae. Comparative genomic analysis further identified 3584 contracted gene families. Branch-site modeling identified 277 genes experiencing positive selection, which may facilitate the adaptation to rocky reef environments. The genome reported here is helpful for ecological and evolutionary studies of H. analis.