After the 1st appearance of Japanese encephalitis virus (JE) on mainland Australia in 1998, astudy was undertaken to investigate whether JE had become established in enzootic transmission cycles onwestern Cape York Peninsula. Adult mosquitoes were collected during the late wet season from Kowanyamaand Pormpuraaw in April 1999, and Pormpuraaw and Barr's Yard in April 2000. Despite processing 269,270mosquitoes for virus isolation, no isolates of JE were obtained. However, other flaviviruses comprising MurrayValley encephalitis virus, Kunjin virus, Alfuy virus, and Kokobera virus (KOK) were isolated. lsolaies of thealphaviruses Ross River virus, Barmah Forest virus (BF), and Sindbis virus (SIN) also were obtained. Themajority (88%) of isolates were from members of the Culex sitiens subgroup. Single isolates of KOK, BF andSIN were obtained from Ochlerotatus vigilax, Oc. normanensis, and Anopheles bancroftii, respectively. Theisolations of flaviviruses during the late wet season indicate that conditions were suitable for flavivirus activityin the area. No evidence was found to suggest that JE has become established in enzootic transmission cycleson western Cape York, although study sites and field trips were limited.