Phylogenetic relationships of 31 pomacanthid species representing all genera were investigated by horizontal starch gel electrophoresis. Nei's genetic distances (D) were calculated and dendrograms constructed from allozyme variation in 23 loci. The average D value was 0.03 between conspecific colour variants, 0.40 between congeneric subgenera, and 1.27 between confamilial genera. From the dendrograms the following were revealed: (1) the generic status of Apolemichthys arcuatus and Holacanthus venustus, as well as the generic and subgeneric status of Centropyge multifasciata were confirmed; (2) the subgeneric status of Xiphypops was confirmed; (3) Pygoplites diacanthus was found to be closely related to members of the subgenus Pomacanthus; (4) Pomacanthus zonipectus was found to be biochemically distinct from its con-subgeners; (5) the genera Pomacanthus and Holacanthus are more closely related than currently thought; (6) the Genicanthus species might warrant a subfamily of their own.