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Despite the prevalence of sclerophyllous vegetation in Australia, there are few phylogeographic studies with continent-wide sampling addressing questions about the expansion of this vegetation post-aridification, and what physical barriers are associated with breaks in distribution or patterns of genetic structure. We used amplicon sequencing of plastid and nuclear DNA to investigate phylogeography of Xanthorrhoea. Despite extremely low genetic variation and widespread sharing of identical DNA sequence among multiple species and across significant geographic distance, haplotype analyses showed phylogeographic structure. Network analysis of six plastid loci and 137 samples identified 54 haplotypes (two common, 35 unique to single samples) in three geographic groups, south west and central Australia, northern–eastern Australia, and southern–eastern Australia, indicating restricted gene flow among regions. A nrDNA haplotype network of 152 samples showed less variation, with one haplotype being widespread, found in all three plastid geographic groups and 70% of species. nrDNA indicated four groups in a pattern, suggestive of at least two east–west divergences. A geographic area of a high haplotype diversity and divergence was identified in southern New South Wales, near the Southern Transition Zone. Our results showed the value of targeted amplicon sequencing and using multiple samples per species to identify both broad-scale and fine-scale biogeographic patterns.