The tomato hind Cephalopholis sonnerati (Valenciennes) (Serranidae), belonging to the genus Cephalopholis, is a bottom dwelling coral reef of 12–120-m depth in the Indo-Pacific and Red Sea. C. sonnerati has also been characterized by complex social structures and behavioural mechanisms. However, due to the lack of genomic resource for C. sonnerati, molecular-genetic studies and genomic breeding remain unexplored in this species. In this study, we reported the chromosome-level genome assembly of C. sonnerati using PacBio sequencing and Hi-C sequencing technologies. We obtained a total length of 1043.66 Mb with an N50 length of 2.49 Mb, containing 795 contigs assembled into 24 chromosomes. Overall 95.8% of the complete BUSCOs were identified in the assembled genome, suggesting the completeness of the genome. Then, we predicted 26,130 protein-coding genes, of which 94.26% were functionally annotated. In addition, C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. Finally, we found tissue-specific expression of 8,108 genes. Functional analyses showed that they mainly consisted of complement and coagulation cascades, DNA replication, synaptic vesicle cycle, long-term potentiation and other glycan degradation. Furthermore, comparative genome analyses indicated that the expanded genes families were highly enriched in the sensory system, which was different from the enrichment analysis of the tissue-specific expression genes. In brief, to our knowledge, we reported the first chromosome-level genome assembly of C. sonnerati, which will provide a valuable genome resource for studies on the genetic conservation, resistance breeding, and evolutionary of C. sonnerati.