Japanese encephalitis virus (JEV), a mosquito-borne pathogen, is the most important cause of viral encephalitis worldwide. The major vector mosquito of this virus, known as Culex tritaeniorynchus, is mainly live in paddy rice field in Korea. So Japanese encephalitis (JE) is a disease of rural areas. During urbanization, rice cultivated land has decreased also resulting the number of JE patients has decreased. However, recent outbreak of JE in Korea 2010, the patients distribution was not related with that of the mosquito. Therefore, this study was conducted to evaluate involving other mosquito species in the transmission of JEV. Five localities, JE reported in 5 years, have been selected to collect mosquitoes according their habitats (mountain, swap, cow shed, and downtown area) in 2012. Total 22,774 collected mosquitoes were pooled by species, date and site of collection. Of the 1,282 pools, eight (five were from Culex orientalis, one from Culex pipiens complex, and two from Aedes vexans) were found positive for flavivirus RNA in SYBR Green I-based real-time RT-PCR assay. The results of sequences blasting on NCBI showed that the flaviviruses from Cx. orientalis and Cx. pipiens complex were identified as JEV genotype V.