The smelt genus Retropinna nominally includes three small (<150 mm) freshwater fish species endemic to south-eastern Australia and New Zealand. For the two Australian species, the broad range of R. semoni (Weber) on the mainland suggests some vulnerability to isolation and genetic divergence, whereas the apparent confinement of R. tasmanica McCulloch to Tasmania is curious if, as suspected, it is anadromous. Analyses of Australian material using allozyme electrophoresis show five genetically distinct species with contiguous ranges and no evidence of genetic exchange. Three occur along the eastern seaboard (including three instances of sympatry), another in coastal and inland south-eastern Australia and Tasmania, and a fifth species in the Lake Eyre Basin. There is no indication of a simple ‘tasmanica’ v. ‘semoni’ dichotomy, but instead a complex pattern involving discrete clusters for the Upper Murray plus Darling rivers, Lower Murray, Glenelg River and Tasmanian regions, with coastal western Victorian samples having varying affinity to these groups. The overall pattern is one of deep divergences among species and strong genetic sub-structuring within and provides a strong argument for extended studies to prepare for appropriate conservation measures.