Phylogenetic reconstructions derived from analyses of DNA sequence variation in a segment of the mitochondrial ribosomal RNA (16S) gene revealed an extensive radiation of species within the genus Branchinella from Australia. Genetic differentiation was evident among all of the species analyzed, including two recently discovered species. There was limited agreement, however, concerning taxon affinities deduced from the 16S data and a previous morphological study. Members of the genus appear to have diversified rapidly, but analyses of other genes and broader taxon sampling are crucial to confirm this hypothesis. Disparities between levels of morphological and molecular change were noted between certain taxa. Whether the radiation of Australian Branchinella happened in situ or was the product of independent colonization events will require the analysis of branchinellids that occur outside Australia.