The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the southern hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as a number of relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, a number of hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias are examined. While most workers consider Lepidogalaxias to be an unusual scaled member of the southern hemisphere galaxioids, it has also been suggested that this species is related to the northern hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid; the alternative hypothesised esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae and the loss of this migratory phase may be a major cause of speciation.