Serological surveys have shown that wild raccoons are exposed to influenza A viruses (IAVs); however, no genetic evidence for this IAV infection has been found. In the present study, we first detected IAV genes in wild raccoons captured during periods other than the wintering season of migratory waterfowl and epidemic season of influenza in Japan. Viral matrix (M) and nucleoprotein (NP) genes were detected by a conventional reverse transcription-polymerase chain reaction assay from three suckling siblings and one juvenile without any noticeable clinical signs, although the NP gene could not be detected from one sibling. The sequences of M gene fragments detected from the rectal swabs of three suckling siblings were comparable with each other but different from those detected from the nasal swab of the juvenile raccoon caught from a different site. The sequences of NP gene fragments detected from two suckling siblings were also comparable. These genetic evidences suggest that IAV is maintained among raccoon populations in the northern part of Japan. Further genetic and virological investigation of IAV infection in wild raccoons is needed to better understand the IAV ecology in the field.