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The Australian arid zone is well recognised as a source of evolutionary novelty and diversity. Roles for selection vs. drift in the region remain less understood. We surveyed mitogenomic diversity and genome-wide nuclear markers in the Mulga Parrot (Psephotellus varius) to add to phylogeographic data from arid zone species. We found structured diversity either side of the Flinders Ranges-Lake Eyre Basin (Eyrean barrier; net nucleotide divergence 1.92% for ND2). Coalescent analysis suggests that this arose during the mid-Pleistocene approximately 402 000 years ago. In both phylogroups, however, the mitogenome is under pervasive purifying selection. Purifying selection in the context of consistent environments either side of the Eyrean barrier may have maintained ancestral plumage and morphological traits, though in other plumage traits there is some plumage divergence that is geographically concordant with the phylogeographic structure. This leads to the essentially ’cryptic’ genetic diversity uncovered here, despite indications of ongoing adaptation to aridity in P. varius as evidenced by increasing bill surface area (shown by earlier work to have increased relative to body size by 10.4% since 1871), a result we affirm here across the species as a whole. This study also demonstrates the utility of shallow ’genome skimming’ sequencing for population analyses.