Culex flavivirus (CxFV) is an insect-specific flavivirus that was first reported in 2007 in Japan. CxFV strains were isolated from Culex tritaeniorhynchus Giles and Culex pipiens L. group mosquitoes and genetically characterized in Toyama Prefecture, Japan, from 2004 to 2009, to reveal host specificity, mode of transmission, and seasonal and geographical distribution. The minimum infection rate (MIR) of CxFV within Cx. tritaeniorhynchus populations was 0.3 and much lower than that within Cx. pipiens group (17.9). The complete genome sequences of 11 CxFV isolates (four from Cx. tritaeniorhynchus and seven from Cx. pipiens group) consisted of 10,835–10,837 nucleotides. When these 11 isolates and five reference strains (NIID-21-2 and Tokyo strains from Japan, Iowa07 and HOU24518 strains from the United States, H0901 strain from China) were compared, there were 95.2–99.2% nucleotide and 98.1–99.8% amino acid identities. Phylogenetic analysis showed that the 11 isolates were divided into four clusters. One cluster consisted of five isolates from Cx. pipiens group and Cx. tritaeniorhynchus from one site and their nucleotide sequences almost completely matched. One cluster consisted of an isolate with a unique sequence from a Cx. pipiens group mosquito captured in an aircraft from Taiwan, suggesting that it was introduced from abroad. CxFV strains were divided into several groups according to countries when nucleotide sequences of CxFV available in GenBank and 11 Toyama isolates were compared. These results suggest that CxFV is maintained in nature among Culex mosquitoes in a mosquito habitat-specific but not a species-specific manner.