Dawson's burrowing bee is a large, fast-flying solitary nesting bee endemic to the arid zone of Western Australia. In this study the population structure of the species was examined with molecular markers. Using eight microsatellite loci, we genotyped 531 adult female bees collected from 13 populations of Dawson's burrowing bee, Amegilla dawsoni, across the species range. The mean number of alleles per locus ranged from 4 to 38 and expected heterozygosity was uniformly high with a mean of 0.602. Pairwise comparisons of FST among all 13 populations ranged from 0.0071 to 0.0122 with only one significant estimate and an overall FST of 0.001. The entire sample collection was in Hardy–Weinberg equilibrium and there was no evidence of inbreeding with a mean FIS of 0.010. The mating and nesting behaviour of this bee suggests that gene flow would be limited by monandry and the fact that almost 90% of females mate immediately on emergence. Nevertheless there is obviously sufficient gene flow to maintain panmixia, and we suggest that this results from infrequent and unreliable rainfall in the species range, which causes the bees to congregate at limited food resources, allowing a small number of unmated females from one emergence site to come into contact with males from another population. In addition, when drought eliminates food resources near an emergence site, the whole population may move elsewhere, increasing gene flow across the species range.