The use of DNA sequences to read the footprint of evolution has grown explosively in the last 25 years. In this paper, DNA sequences are used to understand how the present-day genetic diversity of bird species in southern Australia has been shaped by both environmental forces and the ecology of the birds themselves. While affirming expectations that species of wetter habitats were isolated between eastern and western Australia much earlier than species of drier habitats, we also see how species that move widely in search of food have less genetic structure than more sedentary species. In addition, this paper also argues the need for changes to how we classify some birds. We are suggesting that some birds considered as one species until now need to be recognised as two species. In other cases, we can pinpoint where more work is needed before such a decision can be made.