Australia harbours a rich and unique array of avian species that vary in phenotype across their geographic ranges. By analysing species genes it is possible to identify the evolutionary processes that have shaped this diversity. The five currently-recognised subspecies of the grey shrike-thrush (Colluricincla harmonica) have been classified based on phenotypic distinctiveness. Whether these subspecies represent independently evolving units or just the product of selection on a few phenotypic traits is unclear. Here, multi-locus phylogeography was employed to address this knowledge gap and to identify the processes that influenced species evolution. This was achieved by (1) assessing the genetic distinctness of each subspecies (2) testing the genetic diversity within subspecies and the degree of differentiation between them (3) estimating divergence times among subspecies and (4) estimating gene flow among subspecies. The subspecies were found to be genetically distinct and to experience low rates of migration among them. The phylogenetic breaks and approximate divergence times among subspecies are concordant with the impacts of putative biogeographical barriers that formed during the Pleistocene. These findings indicate that the subspecies have unique evolutionary histories that have likely been influenced by Pleistocene environmental change. Furthermore, C. harmonica lineages are shown here to be distinct, suggesting that they are independently evolving units that may represent incipient species. A genome-wide analysis of genetic diversity would provide further insight into the historical processes and selective forces that have shaped the evolution of C. harmonica.