This study used allozyme and mtDNA variation to examine genetic structure in Rhadinocentrus ornatus and Hypseleotris compressa in southern Queensland. The aim of this study was to test the hypothesis that dispersal between coastal streams was greater in R. ornatus than in H. compressa and to test whether R. ornatus would reflect a similar pattern seen in another obligate freshwater fish in the same region, that is, R. ornatus will show genetic homogeneity among streams of the Sunshine Coast but significant differentiation among all other streams. Evidence from the current study suggests that, in R. ornatus, there was significant genetic differentiation among populations within regions, which explains why this species has very restricted dispersal abilities between streams, even between those very close to one another. On the other hand, H. compressa showed very low levels of genetic differentiation suggesting some gene flow among regions by virtue of dispersal. High levels of genetic differentiation were identified between all coastal streams in the area, including those hypothesized to have been recently connected in the Sunshine Coast area in the case of R. ornatus.