Centropyge bicolor is a tropical marine water fish and widely distributed coral reef fish species with special bicolored body. Because its color and appearance style, it is a kind of popular ornamental fish. However, the whole genome information about bicolored body developing is limited. Here we de novo assembled the first chromosome-level genome as reference with a total length of 650 Mb. The assembled genome was highly contiguous with contig N50 of 114 Kb and scaffold N50 of 4.4 Mb. We identified 21,774 protein coding genes, which were clustered to 16,219 gene families. Furthermore, we identified several candidate gene families associated with its bicolored body developing. Here, as we are known, our study is the first provides a chromosome-level genome as reference for the family Pomacanthidae, which would contribute to the future researches of colorful fish.