The biogeographic history of three cirrhitoid species pairs with east–west allopatric distributions across southern Australia was examined by determining levels of mitochondrial DNA sequence divergence and applying molecular clock calibrations. Similar levels of genetic divergence were observed for Aplodactylus Valenciennes and Goniistius Gill species pairs, but these were more than twice that observed for a Nemadactylus Richardson pair. Molecular clock calibrations suggested divergences occurred during the late Miocene and mid Pliocene, respectively. Given evidence of high dispersal capabilities, the habitat and climatic barriers of the Australian south coast appear too small to have facilitated speciation of the cirrhitoids examined. A mechanism is proposed by which ancestral cirrhitoids were vicariantly isolated into east and west coast populations during periods of climate change. Although Aplodactylus and Goniistius divergences occurred during the same period, separate vicariant events across the Australian north and south coasts are invoked.