Although the platypus, Ornithorhynchus anatinus, is regarded as a single species, there is morphological, behavioural and genetic variation across its geographical distribution. Recent mitochondrial and nuclear DNA studies have revealed at least three evolutionarily significant units within the species. However, it is unclear whether the genetic structures and differences between the documented evolutionary lineages have resulted in gene and/or genome-wide variations which could provide insight as to selection. Here we present a collaborative research project plan between two Australian universities and the University of Oxford to sequence the genome of platypuses from across Australia representing the documented evolutionary lineages. This population analysis study is one part of a large project which will address several other fundamental questions on monotreme genome biology and evolution. We aim to whole-genome sequence 40-50 animals from Queensland, New South Wales, Victoria and Tasmania, some of whom have already been sequenced. The datasets will be aligned and mapped for population genetic analyses and selection tests. Our data will provide valuable insights on population structure, history and genes that may have undergone selection.