In Asia, Culex mosquitoes are of particular interest because of their role in maintaining endemic mosquito-borne viral diseases, including the Japanese encephalitis virus (JEV). Nonetheless, host-feeding preferences, along with naturally infecting RNA viruses in certain Culex species, remain understudied. In this study, selected blood-fed mosquitoes were processed for avian and mammalian blood meal source identification. Concurrently, cell culture propagation and high-throughput sequencing (HTS) approaches were used to determine the RNA virome of Culex mosquitoes collected in Ishikawa Prefecture, Japan. The identification of blood meal sources from wild-caught Culex spp. revealed that Culex (Culex) tritaeniorhynchus Giles, 1901, has a robust preference toward wild boar (62%, 26/42), followed by heron (21%, 9/42). The other two species, Culex (Oculeomyia) bitaeniorhynchus Giles, 1901, and Culex (Culex) orientalis Edwards, 1921, showed a distinct preference for avian species, including migratory birds. From the HTS results, 34 virus sequences were detected, four of which were newly identified virus sequences of unclassified Aspiviridae, Qinviridae, Iflaviridae, and Picornaviridae. The absence of observable cytopathic effects in mammalian cells and phylogenetic analysis suggested that all identified virus sequences were insect-specific. Further investigations involving other mosquito populations collected in different areas are warranted to explore previously unknown vertebrate hosts that may be linked to JEV dispersal in nature.