The three species of emu-wrens (Maluridae : Stipiturus) are small passerines found in arid to mesic habitats across southern Australia. The geographical distribution of nucleotide sequence diversity of mitochondrial DNA (mtDNA) in emu-wrens was investigated to assess the systematic status of Stipiturus (Aims 1 and 2), particularly in eastern Australia, and to examine closely the population structure of Southern Emu-wren (S. malachurus) in the Mount Lofty Ranges of South Australia (Aim 3). Aim 1: Phylogenetic relationships among the three species of Stipiturus, based previously on plumage and allozyme data, are confirmed by our mtDNA data, which support recognition of Mallee Emu-wren (S. mallee) as a distinct (evolutionary) species from, and sister lineage to, Rufous-crowned Emu-wren (S. ruficeps) rather than Southern Emu-wren. These relationships indicate that any interaction between Mallee and Southern Emu-wrens in south-eastern South Australia is a secondary contact. Aim 2: Within the Southern Emu-wren, which currently comprises eight subspecies, phylogenetic relationships among haplotypes from eastern Australia are not concordant globally with subspecies boundaries, but correspond in part to the most recent classification. A quantitative statistical evaluation of the taxonomic implications of phenotypic variation in these birds is warranted. Eastern haplotypes of Southern Emu-wren show strong phylogeographic structure indicative of allopatric divergence in refugia, with subsequent expansion without widespread introgression. Aim 3: Within the endangered populations of the Mount Lofty Ranges, historical isolation and demographic independence of central and southern populations is supported, corresponding with distribution data, but confirmation using nuclear markers is required. Despite separate subspecific designation of emu-wrens of the Mount Lofty Ranges (which are endangered) and south-eastern South Australia, they share mtDNA haplotypes without strong differentiation and emu-wrens of south-eastern South Australia should be preferred over Kangaroo Island birds for translocations into the MLR, although translocation among populations of the Mount Lofty Ranges is probably a wiser initial strategy to minimise the impact of ecological differences and risk of introduction of disease.