The delineation of species and their evolutionary relationships informs our understanding of biogeography and how regional faunas are assembled. The peripheral geography and local environment of reefs in the subtropical South Pacific likely promotes the allopatric and adaptive divergence of taxa colonising from the tropics; however, the fauna of this region has been relatively understudied. Here, we address the taxonomic and evolutionary relationships among Chrysiptera taxa of the subtropical South Pacific. We use meristic counts, morphometrics and genetic markers to characterise the similarities and differences among four taxa restricted to the South Pacific region that have strikingly different colouration: C. notialis, a taxon restricted to eastern Australia, New Caledonia, Lord Howe Island and Norfolk Island; C. galba, found in the Cook Islands, southern French Polynesia and Pitcairn Islands; and the two disjunct populations of C. rapanui, found in the eastern Pacific around Rapa Nui (Isla de Pascua or Easter Island) and Motu Motiro Hiva (Salas y Gómez) and in the South-western Pacific around Rangitāhua (Kermadec Islands). Our morphometric analysis confirmed that these four taxa, including the two disjunct populations of C. rapanui , are morphologically distinct. However, our genetic analysis revealed that only C. rapanui from Rapa Nui was genetically differentiated, whereas C. rapanui of Rangitāhua, C. galba and C. notialis all shared a common haplotype. Furthermore, none of the taxa could be consistently differentiated based on individual meristic features. Our study reconciles a formerly perplexing and disjunct distribution for C. rapanui , to reveal that C. rapanui is an endemic of Rapa Nui and that the Chrysiptera of French Polynesia, Rangitāhua, and the South-western Pacific have only a very recent history of divergence. Our analyses suggest these subtropical taxa have diverged from a predominantly tropical Chrysiptera genus in morphological features important in determining colonisation success, locomotion and feeding ecology.