The Lake Eyre Basin in the central Australian arid zone is one of the harshest environments freshwater fishes inhabit. Waterholes are often the only available habitat for riverine species, but this habitat becomes greatly limited during drought periods, and within some river basins almost all waterholes have dried at least once in the past 200 years. Fish species in the Basin range from specialised endemics, to widespread generalists found across Australia. Generalists are expected to utilise a resilience strategy to persist, where they are able to rapidly disperse and recolonise habitat when conditions improve, while specialists are able to withstand extreme conditions – a resistance strategy. This study uses genetic techniques to investigate the population ecology of three generalist fish species (bony bream Nematalosa erebi, barred grunter Amniataba percoides, and spangled perch Leiopotherapon unicolor), sampled across the Basin’s river systems. Preliminary results, based on mitochondrial sequence data, show little genetic diversity within river systems, but significant variability among them. This suggests that populations in different drainages are functionally isolated and subject to genetic bottlenecking and drift, counter to expectations that these taxa would show significant gene flow due to high mobility. Further analyses of additional mitochondrial and nuclear sequence data, and comparisons with two resistant taxa (desert goby Chlamydogobius eremius, and Lake Eyre hardyhead Craterocephalus eyresii), will also be presented.