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The circulation and infection of avian influenza virus (AIV) in zoos and backyard flocks has not been systematically investigated. In the present study, we surveyed the birds including those in live bird markets (LBMs) and evaluated co-circulation of AIVs among them. Overall, 26 H9N2 AIVs and one H6N2 AIV were isolated from backyard flocks and LBMs, but no AIVs were isolated from zoo birds. Genetic analysis of the HA and NA genes indicated that most of the H9N2 AIVs showed higher similarities to AIVs circulating in domestic poultry than to those in wild birds, while the H6N2 AIV isolate from an LBM did to AIVs circulating in migratory wild birds. In serological tests, 15% (391/2619) of the collected sera tested positive for AIVs by competitive-ELISA. Among them, 34% (131/391) of the sera tested positive for AIV H9 antigen by HI test, but only one zoo sample was H9 positive. Although AIVs were not isolated from zoo birds, the serological results indicated that infection of AIVs might occur in zoos. It was also confirmed that H9N2 AIVs continue to circulate and evolve between backyard flocks and LBMs. Therefore, continuous surveillance and monitoring of these flocks should be conducted to control further epidemics.