Anopheles farauti s.s. is an important malaria vector of the southwest Pacific region (SWP) and one of 12 cryptic species in the An. punctulatus group. From collections spanning northern Australia, Papua New Guinea, the Solomon Islands and Vanuatu, we looked at the population genetic structure of this coastally restricted malaria vector using the mitochondrial cytochrome oxidase gene (COI) and the ribosomal DNA transcribed spacers 1 and 2 (ITS1 and ITS2). We found this mosquito to be made up of several geographically and genetically structured populations with barriers to movement identified between islands as well as within the continents of Australia and Papua New Guinea. The concerted evolution if the ITS1 and ITS2 suggested substantial non-homogenised spacer variation fixed within populations and showed a much more rapid, but less quantitative, evolution than the COI.