The fish fauna of eight aquatic habitats of the dune fields of Cape Flattery, northern Queensland was surveyed by electrofishing, seine-netting, bait trapping and line fishing. Fifteen species from eight families were collected and reference to a further three species was found in the literature. The composition of the fauna present in dune lakes of the region differed from that occurring in other habitats (streams and pools), containing additional species of larger body size and piscivorous habit. All of the species collected were in the non-threatened category with respect to their conservation significance, although many of the species exhibit highly disjunct distributions. The presence of previously unknown populations of such species in the dunefields of Cape Flattery may warrant reexamination of the conservation status of these species and of the significance of the region. An assemblage of fishes indicative of oligotrophic acidic stained waters of northern Queensland was identified. The fish fauna is regionally distinctive compared to those found in similar habitats elsewhere in Queensland.