In order to explore the genetic variation and molecular characteristics of H9N2 subtype avian influenza viruses in Shanghai, fourteen H9N2 subtype avian influenza viruses were isolated from live poultry markets, poultry farms and pig slaughterhouses in 2002 and 2006－2014. These specimens included paired tracheal and cloacal swabs from chickens, ducks, pigeons and domestic wild chickens and lung samples from pigs. They were determined as H9 subtype by real－time reverse transcriptase－polymerase chain reaction (RT－PCR) and then isolated by using 10－day－old specific pathogen free chicken eggs, further identified as H9 subtype by hemagglutination inhibition (HI) test. The eight gene segments of the fourteen virus strains were amplified by RT－PCR and sequenced. Phylogenetic analysis revealed that the isolates were reassortants mainly of A/chicken/Shanghai/F/1998, A/duck/HongKong/Y280/1997, A/quail/ HongKong/G1/1997. Five virus strains isolated from 2002 and 2006－2008 represented four different genotypes. The other nine virus strains isolated in 2008－2014 was different from the above four genotypes. This may be related to the pressure of immune selection by vaccine.