Carrion-breeding blowflies have substantial ecological and forensic importance. Because morphological recognition of their immatures is difficult, sequencing of the mtDNA of these flies may assist with their identification. Molecular phylogenetic analysis based on DNA sequences can also clarify evolutionary relationships. In this study, the mitochondrial genes CO1, CO2, ND4 and ND4L were sequenced for 34 species of blowflies, among which are almost all species known or suspected to breed in carrion in Australia. The resulting sequences were analysed using parsimony and maximum-likelihood Bayesian techniques. The results showed that the combination of these four genes should identify most species reliably, although some very closely related taxa could still be misdiagnosed. The data also helped clarify the life histories of Calliphora centralis Malloch, 1927, C. fuscofemorata Malloch, 1927 and C. gilesi Norris, 1994, which have hitherto only been suspected carrion breeders, and revealed that the current subgeneric assignment of taxa within Calliphora Robineau-Desvoidy, based on morphology, requires revision. Unexpectedly, both Chrysomya rufifacies (Macquart, 1843) and Lucilia cuprina (Wiedemann, 1830) were paraphyletic; each probably comprises two distinct species. The application of a molecular-clock approach to the study of the evolutionary divergence of the carrion-breeding blowflies suggests that the speciation of at least the endemic Australian taxa may have been the result of increasing aridification in Australia during the last five million years.