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The phylogeographic structure of the widely distributed arid and semi-arid Australian splendid fairy-wren Malurus splendens was investigated by using variation in plumage characters and mitochondrial DNA (mtDNA). We examined sequences of the mtDNA ND2 gene and used spectrophotometry to quantify chromatic variation in plumage in order to test the current morphology-based intraspecific taxonomy of M. splendens and to discriminate between hypotheses invoking allopatric and parapatric processes in the origin of diversity in the complex. Genetic diversity of M. splendens fell into three divergent geographically structured clades. One represents populations ascribed to the western subspecies M. s. splendens, the other populations of central M. s. musgravi and the third all eastern populations currently ascribed to M. s. emmottorum and M. s. melanotus. Plumage patterns clearly differentiate M. s. splendens and M. s. musgravi, and spectrophotometry identified a step-wise transition in spectra between M. s. melanotus and M. s. emmottorum. Congruence of patterns of phenotypic and genetic variation among western, central and eastern populations of M. splendens strongly suggests that these populations have diverged in allopatry on either side of historical biogeographic barriers in this region. Decoupled patterns of phenotypic and genetic diversity suggest that the divergence of M. s. melanotus and M. s. emmottorum may have occurred without periods of isolation perhaps in response to differences in local environmental conditions, or alternatively, mtDNA and plumage may have different rates of evolution. Critically, we encountered issues with the placement of the root of the M. splendens complex. The root was placed within the subspecies M. s. splendens separating its northern and southern populations and rendering the subspecies paraphyletic.