In the Australian arid zone, aquatic habitats exist as isolated waterholes, connected only intermittently by occasional floods. Gene flow among populations of aquatic insects in this boom and bust environment depends, in part, on how well animals can disperse across large and often inhospitable distances. We investigated differences in genetic structuring between seven species of strong or weak-flying dispersers, and hypothesized that strong-flying aquatic insects would exhibit less genetic structuring than weak-flying taxa.  We analysed up to 1000 anonymous nuclear markers per individual to identify fine-scale patterns of gene flow among spatiotemporally disconnected populations from the central Australian outback. Results from a preliminary study using single mitochondrial and nuclear DNA sequence markers indicate significant variation among populations of weakly dispersing species, while strong dispersers display minimal spatial genetic subdivision. However, the large volume of anonymous loci used in the current study will provide much more precise estimates of dispersal, gene flow and timing of these events among populations. A better understanding of the phylogeographic structuring of arid Australia’s aquatic fauna is a critical step in on-going conservation and management efforts.