Abstract: Objective The study was designed tO study the genetic characteristic of HA of epidemic strain for influenza A virus in Shanghai City between 1990 and 2004，and explore the relationship between the genetic variation of influenza virus and flu epidemic．Methods The two methods of chick embryo and MDCK cell were used to separate the influenza A virus．Virus RNA was extracted for purification of amplified products of Reverse Transcrpfion Polymerase Chain Reaction(RT-PCR) and determination of nucleotide sequence，and the‘MegAlign software was adopted for analysis of phylogenetic tree．Results From 2000.compared with A/Sydney/5/1997 (H3N2)and A/Wuhan/359/1995(H3N2)，the nucMotide homology in the Hal area for H3N2 prevalent in Shanghai City was 95.7％-98.6％ and 96.8％-98.6％ respectively．And that compared with H3N2 prevalent in 1990s was 88.4％-92.8％．And the replacement of amino acid took place in the areas of A，B，E and D of antigenic determinant and left arm of receptor binding site(RBS)，while compared with A/HongKong/1131/1998 (HINl)and A/Shanghai/7/1999(H1N1)，the nucleotide homology for the H1N1 was 97.8％-99.3％．And that compared with H1N1 prevalent in 1990s was 96.8％-97.8％．The phylogenetic tree showed that in recent years there existed a branch for influenza A virus of genetic characteristic different from that of epidemic strains in 1990s．Conclusion There has been no apparent variation for antigenicity of H1N1 in Shanghai City since 2000，but the gene of influenza A (H3N2) virus is mutated，and the antigehicity iS SO shifted．Which iS the main reason for lOCal outbreak of influenza in recent years．