Here we present the genome assembly for the three-spot damselfish, the first within its genus in the widely studied and large Pomacentridae family. This genome was assembled using a combination of ONT, HiC and Chicago reads, as well as Illumina shotgun data. The three-spot (or domino) damselfish (Dascyllus trimaculatus) is a tropical reef associated fish within a species complex which includes at least three other described species. Of all of them, D. trimaculatus has the broadest range, extending from the Red Sea, where it was first described (Rupell), across the tropical and subtropical Indo-Pacific. The high quality genome of this non-model coral reef fish is a valuable reference for furthering studies of evolutionary, ecological, and conservation studies.