Hypseleotris includes eight described and four undescribed species of small, laterally compressed gobioid fishes, unusual among them in that they superficially resemble cyprinids. One species is widespread throughout the fresh and brackish waters of the old world southern hemisphere; the remaining eleven species form a radiation in Australia and southern New Guinea. In this study, morphological and molecular characters are combined in a total evidence phylogenetic analysis in order to investigate the patterns of diversification in Australian and other Hypseleotris, including a consideration of biogeography. The species H. dayi, H. tohizonae, H. leuciscus, and H. guentheri are synonymized with H. cyprinoides. Within Australian Hypseleotris, H. klunzingeri is the most basal taxon, and the remainder of the species fall into two groups: a radiation in Western Australia and the Northern Territory, and a second radiation in the eastern, central, and southeastern river drainages.