As the driest inhabitable continent, it comes as no surprise that Australia has comparatively few species of freshwater-dependent fishes compared with land masses of similar size and latitudinal coverage. In addition to relatively low rainfall and few permanent waterbodies, a range of other climatic, geological, physical, and biogeographical factors are generally offered up, to account for the low species count in a country otherwise regarded as mega-biodiverse. Here, we challenge this traditional view by hypothesising that Australia's lack of freshwater fishes largely reflects a dearth of detailed taxonomic activity. Using both allozyme and mtDNA markers, we undertook a molecular assessment on the Australian purple-spotted gudgeons (Mogurnda), recently subjected to a taxonomic revision that saw a three-fold increase in the number of described species. In addition to demonstrating additional, species-level biodiversity within M. adspersa, our genetic data revealed discordant patterns of mitochondrial and nuclear genetic affinities among populations in several species, plus a sister relationship between the two central Australian species. We discuss the broader implications of such cryptic biodiversity for the Australian freshwater fish fauna; most notable among these is our prediction that only 50% of species have been described.