Freshwater organisms are often hypothesized to reflect the hierarchical nature of stream channels in the genetic structure of their populations. However, patterns of genetic structure are also affected by the dispersal mechanism of the particular species and the nature of the river channels. In this study, the genetic structure of a freshwater crayfish, known to have the ability for terrestrial dispersal, was examined in a habitat where stream structure and elevational differences across catchment boundaries are minimal. It was found that levels of connectivity among populations in the same catchment are high, suggesting either recent or contemporary dispersal among them. In contrast, almost no sharing of haplotypes across drainage boundaries indicates limited terrestrial dispersal across them. However, nested clade analysis indicated that, historically, there has been movement between drainages. It is suggested that populations in the Cooper and Murray-Darling were isolated in the past and that, more recently, recolonization has occurred in an east-west direction from the Murray-Darling to the Bulloo and from the Bulloo to the Cooper. These movements probably occurred in wetter times when whole catchments were flooded.