Brown-marbled grouper (Epinephelus fuscoguttatus) is an important fish species for coral reef ecosystem and marine aquaculture industry. In the study, a high quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximate 42% and 0.35 %, respectively in brown-marbled grouper genome. A total of 230 contigs with total length of 1,047 Mb were assembled, contig N50 was 13.8 Mb, 228 contigs (99.13%) can be anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among of them, 23,862 (99.4%) predicted genes were annotated. The high quality chromosome-level genome of brown-marbled grouper will provide pivotal genetic foundation for further researches of grouper.