We report on the genetic structuring of populations of a large burrowing frog, Heleioporus albopunctatus, from the central wheatbelt of Western Australia. This region has been highly fragmented by vegetation clearance for agriculture since the early 1900s. Genetic variation at four variable loci in 22 populations was analysed using cellulose acetate electrophoresis. Analysis across all populations showed a moderate, but significant, degree of subdivision (F-st=0.087 +/- 0.049, P<0.05) and high levels of heterozygosity (H=0.133, s.e.=0.084). Several small populations had higher F-st values in pair-wise comparisons. A mantel test revealed no significant relationship between genetic distance and geographic distance (r=-0.136, P=0.34) and this, combined with data from multidimensional scaling analyses, suggests that geographic isolation of populations is not a significant determinant of genetic structuring. Despite this, the presence of high levels of subdivision as a result of the erosion of genetic diversity indicates that regional persistence may be dependent on the maintenance of metapopulation structures that allow gene flow.