The queen angelfish was first described as Chaetodon ciliaris in 1758 by Carl Linnaeus in the 10th edition of his Systema Naturae, with the type locality given as the "Western Atlantic/Caribbean".[3] In 1802 it was moved by French naturalist Bernard Germain de Lacépède to the genus Holacanthus,[4] the name of which is derived from Ancient Greek ὅλος (hólos), meaning "full", and ἄκανθα (ákantha), meaning "spine".[2] Its specific name ciliaris means "fringed", a reference to its squamis ciliatis ("ciliate scales").[5] Other common names for the species include "blue angelfish", "golden angelfish" and "yellow angelfish".[6]
Marine angelfish of the genus Holacanthus likely emerged between 10.2 and 7.6 million years ago (mya). The most basal species is the Guinean angelfish (Holacanthus africanus) off the coast of West Africa, indicating that the lineage colonized the Atlantic from the Indian Ocean.[7] The closure of the Isthmus of Panama 3.5–3.1 mya led to the splitting off of the Tropical Eastern Pacific species.[8] The closest relative and sister species of the queen angelfish is the sympatric and similar Bermuda blue angelfish (H. bermudensis), from which it split around 1.5 mya.[7][8] They are known to interbreed, producing a hybrid known as the Townsend angelfish[9] which has features similar to both parent species.[10] The Townsend angelfish is fertile, and individuals can breed both with each other and with the two parent species.