Jacky dragons (Amphibolurus muricatus) are ubiquitous in south-eastern Australia and were one of the first Australian reptiles to be formally described. Because they are so common, Jacky dragons are widely used as a model system for research in evolutionary biology and ecology. In addition, their distribution along the Great Dividing Range of eastern Australia provides an opportunity to examine the influence of past biogeographical processes, particularly the expansion and contraction of forest habitats, on the diversification of this iconic agamid lizard. We generated sequence data for two mitochondrial and three nuclear DNA loci (4251base pairs) for 62 Jacky dragons sampled from throughout their distribution. Phylogenetic analyses based on maximum likelihood and Bayesian species-tree methods revealed five geographically structured clades separated by up to 6% mitochondrial and 0.7% nuclear sequence divergence. We also quantified body proportion variation within and between these genetic clades for more than 500 specimens and found no evidence of any significant differentiation in body proportions across their range. Based on body proportion homogeneity and lack of resolution in the nuclear loci, we do not support taxonomic recognition of any of the mitochondrial clades. Instead, A muricatus is best thought of as a single species with phylogeographic structure. The genetic patterns observed in the Jacky dragon are consistent with fragmented populations reduced to multiple refugia during cold, arid phases when forested habitats were greatly restricted. Consequently, the inferred biogeographic barriers for this taxon appear to be in line with lowland breaks in the mountain ranges. Our results are congruent with studies of other reptiles, frogs, mammals, birds and invertebrates, and together highlight the overarching effects of widespread climatic and habitat fluctuations along the Great Dividing Range since the Pliocene.