In 1995 and 1998, outbreaks of Japanese encephalitis (JE) virus occurred for the first time in Australia. Virus isolation from pools of mosquitoes indicated Culex annulirostris Skuse was the most likely vector. It was hypothesized that wind-blown mosquitoes introduced JE from Papua New Guinea to the Torres Strait and Cape York, northern Australia. This study used levels of genetic differentiation, as indirect evidence of dispersal of mosquitoes between the two continents. The results have demonstrated that in the region incorporating Western Province in PNG, the Torres Strait and Cape York Peninsula, Cx. annulirostris is represented by a panmictic population, indicating frequent widespread dispersal throughout the region of investigation. The closely related Cx. Palpalis Taylor was also present at some locations but the population structure of this species is uncertain. This supports the hypothesis that wind-blown Cx. annulirostris and possibly Cx. Palpalis could be a possible mechanism for introduction of JE virus into Australia.