There is limited information about virus epidemiology of shorebirds (family Charadriidae and Scolopacidae) in the East Asia-Australasia flyway. We investigated the prevalence of avian influenza viruses (AIVs) in shorebirds in Hokkaido, Japan, the stopover site of the flyway, to understand the ecology of AIV translocation in the flyway from 2006 to 2010. In total, 1,698 shorebirds belonging to 26 species were captured and released into two different sites using mist nets. Tracheal and cloacal swabs were collected from each bird using cotton swabs. The RNA of influenza A viruses was detected using reverse transcription loop-mediated isothermal amplification. One AIV-positive sample was obtained from a Lesser Sand Plover (Charadrius mongolus) captured in September 2010 at Lake Komuke. Full lengths of hemagglutinin (HA), neuraminidase (NA), polymerase acidic protein (PA), nucleoprotein (NP), matrix protein 1 (MP), and nuclear export protein (NS) genes were successfully amplified from the AIV-positive sample. All sequences showed the highest identity with sequences obtained from virus strains from Anseriformes species. Shorebirds migrated to Japan 1 mo earlier than did Anseriformes species. Therefore, the Lesser Sand Plover could have been infected by the virus from Anseriformes species on the breeding grounds. The HA sequence showed the highest identity with the H10 sequence whereas the NA sequence exhibited the highest identity with the N7 sequence. Phylogenic analysis showed that the detected subtype H10N7 belongs to the Eurasia lineage and the related strain might have widely spread in Asia in 2009.