Wrasses are distributed worldwide in coral reef environments, and display a specialized feature of paired pharyngeal bones united into a single jawbone. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological values. Here, we present genome assembly of C. undulatus, using Illumina, Nanopore, and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb, and anchored to 24 chromosomes. A total of 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were completely represented. Transcriptomic analyses showed to express 96.79% of the predicted gene. Transposons were most abundant, accounting for 39.88% of genome, with low divergence, owing to evolve with close species approximately 58.37 million years ago, and 560/1,848 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Additionally, 46 genes underwent positive selection. Comparative genomic analyses with other fishes revealed unexpected expansion of opsins SWS2, LWS1, and Rh2, showing single-gene expansion up to five copies in tandem arrays. Gene conversion was responsible for abundance of opsin specific for C. undulatus, and the uneven distribution of transposons in opsin windows and adjacent windows probably contributed to gene conversion, providing gene function fluidity. Divergence of opsin expression in tissues indicated alternative adaptations of the increased opsin copies for the visual foraging and sexual behavior. Genome sequencing of the humphead wrasse provides valuable resources for future investigation of conservation, evolution, and functional morphology of fishes.