The Australo-Papuan region is an area containing high levels of endemism and biodiversity. New Guinea in particular is geologically and biogeographically very complex yet there are only a limited number of studies on population structure that have been performed in this region. I will present a comprehensive microsatellite data set from a widespread and biologically interesting mosquito species, Anopheles hinesorum, occurring throughout in this area. I show that there are a number of genetically distinct populations of this species and that some of these populations may in fact be separate species or subspecies as there is no evidence of hybridization or introgression between populations. This work builds on previous phylogeographic work done on the species that revealed strong population structure in this species and evidence that two distinct mitochondrial lineages of An. hinesorum are present on the Solomon Islands. Thus there is evidence for two separate dispersals of this species to the archipelago. Interestingly this species bites humans and transmits malaria in New Guinea but does not in the Solomon Islands, raising questions as to whether this potentially medically significant trait has evolved independently in each of the mitochondrial lineages or whether it was transmitted from one to the other via nuclear gene flow.