The arid-zone is Australia’s largest biome, making up approximately 70% of the continent’s area. Arid-zone freshwater ecosystems encompass a spectrum of water availability, from permanent groundwater-fed springs to ephemeral ponds created by torrential rain. Dispersal allows strong-flying freshwater insects to maintain broad geographical ranges in this environment, despite occupying isolated ‘islands’ of water surrounded by uninhabitable land. In contrast, populations of weak-flying species, become isolated and may diverge genetically but not necessarily morphologically, and may thus evolve into cryptic species. The Australian arid-zone is predicted to increase in area under climate change, with extreme events increasing in frequency and/or intensity. For management purposes it is imperative to understand important processes, such as dispersal, and the extent of cryptic speciation and spatiotemporal distribution of lineages. This study sought to answer two questions: are cryptic species present, and do weaker flyers have more structured populations and use the landscape at smaller spatial scales than do stronger flyers? Individuals from two species of mayflies and two species of dragonflies were collected from eight sites in the Pilbara and sixteen sites in Central Australia. DNA was extracted and each species was screened for variation with at least one mitochondrial and one nuclear sequence marker. Weaker-flying mayfly species had more structured populations, with likely cryptic species present. In contrast, the stronger-flying dragonflies exhibited very low levels of genetic divergence between the Pilbara and Central Australia despite the geographical distance. These results highlight the importance of managing arid-zone water-bodies at both continental and smaller spatial scales.