The Variegated Fairy-wren Malurus lamberti as currently construed occurs across almost all of mainland Australia. If Pleistocene biogeographical barriers limited gene flow in this species, then geographical restriction of haplotypes should mirror those barriers. We used phylogeographic analyses of one mitochondrial and eight nuclear DNA markers to reconstruct the bird’s history, especially for its arid and tropical populations. Robustly supported phylogeographic structure between M. l. lamberti of central eastern Australia and all other populations suggests vicariance by the Great Dividing Range of eastern Australia; time to their most recent common ancestor origin traces to approximately 148 000 years ago (Kya; 95% highest posterior density interval 62–312). Estimates of divergence time for populations of M. l. assimilis east and west of the central southern Australian Eyrean Barrier converged at 86 Kya (45–133), the youngest estimated divergence being between two tropical taxa (14 Kya, 0–30). Taxonomic implications of our data question the current circumscription of M. lamberti, but support taxonomic recognition of structuring east and west of the Eyrean Barrier within what is currently M. l. assimilis. Genetic diversity in two tropical taxa is incompletely sorted or at early stages of divergence with gene flow.