Japanese encephalitis is a disease of major importance in Asia, which from 1995 has extended its range into the north of Australia. Culex annulirostris Skuse of the Culex sitiens subgroup of Culex was incriminated as the most likely mosquito vector. Because misidentifications previously have occurred within this subgroup, our paper defines electrophoretic methods to identify Culex specimens from Queensland and the Northern Territory in Australia and from Western Province in Papua New Guinea. In collections from 1996 to 1998 Culex sitiens Wiedemann, Cx. palpalis Taylor, and Cx. annulirostris comprised 93.1% of the total banded proboscis Culex mosquitoes collected; 6.9% remained unidentified to species by morphological or electrophoretic examination. The prevalence of Cx. palpalis was variable and appeared to be associated with below average rainfall during 1997. In Papua New Guinea, this species comprised up to 97.4% of banded proboscis Culex, with smaller numbers collected from the Torres Strait Islands and Cape York; none was collected from other Queensland localities. Cx. annulirostris was more prevalent during years of average or above average rainfall and was predominant in most localities, especially in the Torres Strait and Queensland. These data confirmed the problems in separating Cx. sitiens from Cx. palpalis and Cx. annulirostris using morphological characters.