The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri , have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna , while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.