We selected one of the most iconic Red Sea butterflyfish species, Chaetodon austriacus, for whole genome sequencing. This species is distributed almost exclusively in the northern and central Red Sea region. Chaetodon austriacus has three closely related sister taxa found together in the Coralochaetodon subgenus, Chaetodon trifasciatus, Chaetodon lunulatus, and Chaetodon melapterus, which live exclusively in the Indian Ocean, Pacific Ocean, and Arabian Sea, respectively. The genome of C. austriacus will provide a scaffold for analyzing apparent patterns in SNP datasets for this and related species, especially loci that appear to be under some form of selection. Annotation will provide a means to identify genes that may control unique adaptations to the Red Sea environment. This project has direct applications to the fields of biogeography, phylogeography, population genetics, meta-population dynamics, and regulating the international exchange of marine resources