Long-distance dispersal might be an important mechanism for the maintenance of aquatic insect populations in heterogeneous landscapes. However, these events can be difficult to measure by direct observation because the techniques can be time-consuming, expensive and technically difficult. When dispersal results in gene flow within and between populations, patterns of variation can be detected by genetic methods. The levels of population genetic structuring and the relationship between gene flow and geographical distance were assessed in the mayfly species Bungona narilla (Harker, 1957) in rainforest streams in south-east Queensland that are separated by lowland habitats. An analysis of molecular variance based on mitochondrial DNA data, using a fragment of the cytochrome oxidase I gene, revealed significant differentiation between regions, suggesting that maternal gene flow was restricted. A nested clade analysis revealed patterns of historical (contiguous) range expansions and recent restricted gene flowalong with some long-distance dispersal events. Our analyses have shown that populations of B. narilla are significantly structured throughout the species range in south-east Queensland and that the low elevation habitats separating the northern and southern populations are restricting gene flow to some extent.