To analyze the relationship between influenza epidemic and genetic characteristic on the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province during 1998 to 2009.All of the eight genes from the 19 Zhejiang influenza virus isolates, circulated during 1998 to 2009, were amplified by RT-PCR and sequenced. The obtained sequences were aligned and analyzed with the vaccine strains being used in the last 10 years.The highest mutation happened within HA and NA genes and the amino acid divergent ratios were 13.98% and 10.00%. Amongst the six internal proteins, the amino acid divergent ratios of NP, M2 and NS1 were 6.43%, 6.19% and 3.48% respectively, and the others were lower than 3%. Other than the HA and NA genes, mutations were also observed on six internal genes of the strains isolated in those years when the influenza virus subtype A/H3N2 was widely circulating. Additionally, there had been an obvious genetic lag between vaccine strains recommended by WHO and the contemporary Zhejiang epidemic strains for many years.Besides on HA and NA genes, surveillance programs should also be covered mutations regarding the internal genes of influenza virus subtype A/H3N2 strains, in order to provide important information for forecasting and warning of a new round of influenza epidemic.