The phylogenetic relationships of the family Pomacentridae (Teleostei: Perciformes) were explored using mitochondrial DNA sequence data from the mitochondrial transfer RNA Phe, 12S mitochondrial ribosomal RNA, and 16S mitochondrial ribosomal RNA genes (1510 base pairs) for 23 species in 14 genera of pomacentrids. Outgroups were drawn from the other three putative families of the suborder Labroidei. Total evidence analyses using both weighted and unweighted parsimony criteria were performed. A weighting scheme was employed to account for site saturation. The results find a monophyletic Pomacentridae and subfamily Amphiprioninae. Premnas is recovered within Amphiprion, thereby rendering Amphiprion paraphyletic. The Chrominae is not monophyletic, because one putative member (Mecaenichthys) appears in a more basal position in the tree. These results do not support a monophyletic Pomacentrinae but rather suggest that it is a polyphyletic assemblage. The genus Pomacentrus appears to be the sister group to the Amphiprioninae. There is support for the monophyly of Abudefduf, Dascyllus, Pomacentrus, and Stegastes. A monophyletic group consisting of the Amphiprioninae, Pomacentrus, Neoglyphidodon, and Amblyglyphidodon was observed. Higher level relationships within the Pomacentridae are not well supported, and additional data are required.