Humpback grouper (Cromileptes altivelis), an Epinephelidae species, patchily distributed in reef habitats of Western Pacific water. This grouper possesses remarkably different body shape and notably low growth rates comparing other grouper species. Up to now, evolutionary status of humpback grouper is ambiguous in grouper species. For promote further research of the grouper, in the present study, a high quality chromosome-level genome of humpback grouper were assembled using PacBio sequencing and high-throughput chromatin conformation capture (Hi-C) technology.