The presence of DNA sequences integrated from a new flavivirus related to Cell Fusing Agent and Kamiti River Virus was identified in wild Aedes albopictus mosquito populations from the provinces of Trentino and Padova, Northern Italy. Field work was developed during August-October 2007 with BG-traps, and mosquitoes were screened for flavivirus and alphavirus. No alphavirus was detected, indicating that Chikungunya virus is not present in these mosquitoes in Trentino and Padova area. However, 21% of the pools were positive for flavivirus, further recognised with BLAST as similar to Kamiti River Virus. Phylogenetical analysis with 708 nucleotides from the NS5 gene identified this virus as a new member of the insect flavivirus clade, together with others like Kamiti River Virus, Cell Fusing Agent or Culex flavivirus, and in the group of those transmitted by Aedes. Furthermore, the treatment with RNAse, indicated that this flavivirus should be integrated in the genome of Ae. albopictus. These results propose that these sequences are transmitted by both sexes, and with different prevalence in the studied populations, and support the idea of a widespread distribution of integrated genomes in several mosquitoes from different areas, as first demonstrated with Cell Silent Agent. Evolutionary implications of this discovery and application in flavivirus phylogeny are discussed.