For proper management and conservation of the Kuril harbor seal (Phoca vitulina stejnegeri) through disease control, serological analysis was performed for influenza A virus infection in free-ranging seals in Hokkaido, Japan. Serum samples were collected from seals at Nosappu (231 seals), Akkeshi (16) and Erimo (75), between 1998 and 2005, and were analyzed by ELISA. Antibodies to the influenza A virus were detected only in seals from Nosappu. The incidences were 11% (1/9), 3% (2/66), 12% (7/59) and 6% (5/77) in 1998, 2003, 2004 and 2005, respectively. These suggest sporadic infection. Because antibody-positive seals included juvenile seals in each year, the infections were considered to have been circulated since no later than the late 1990s until recent years. ELISA-positive sera were analyzed by hemagglutination inhibition (HI) tests to determine the subtypes. Antibodies to the H3 and H6 subtypes were detected in 10 and 2 sera, respectively. Two of the sera that had antibodies to the H6 subtype also had antibodies to the H3 subtype. These two seals were considered to have been infected with both the H3 and H6 subtypes. This is the first investigation to find antibodies to the H6 subtype in seals. Although the H6 subtype had been isolated only from avians, genetic analysis had suggested that the H6 subtype could become a novel mammalian pathogen. For definitive diagnosis, detection of the virus from the tissue or mucus of seals is required.