The Lake Eyre Basin in the Australian arid zone is one of the harshest environments in which freshwater fish are found. Waterholes are often the only available habitat for riverine species, but most of these become uninhabitable during drought periods, and almost all have dried at least once in the past 200 years. For fish species to persist, not all waterholes can be simultaneously uninhabitable, and fish must disperse when possible to maintain a wide geographic range, allowing recolonisation of sites when conditions improve. We will use genetic techniques to investigate the ecological and evolutionary processes operating on these species on a range of timescales. Preliminary results using mitochondrial markers from three species across the Northern Territory and South Australian rivers of the Basin have shown little within-drainage genetic diversity, but significant among-drainage variability. This suggests that populations in each drainage may be functionally isolated and subject to genetic bottlenecking and drift, explicable by the extreme boom-and-bust nature of this system. Further research will expand on this, by sequencing up to 1400 anonymous loci per individual, from populations sampled in replicate drainages across the entire Lake Eyre Basin. Five taxa were chosen to represent a range of hypothesised persistence strategies, from ‘resilience’ (spangled perch, bony bream), to ‘resistance’ (Lake Eyre and Finke hardyhead, Desert and Finke goby), with barred grunter utilising an intermediate strategy. This will allow us to explore the differences among drainages and species, and determine how fish populations persist in this extreme environment.