Abstract: Objective To study the variation and genetic characteristics of hemagglutinin gene HA1 of influenza virus B strains isolated in Jiaxing City since 2011, and evaluate the protective effect of the influenza vaccine strains recommended by WHO. Methods The influenza viruses were isolated by using MDCK cell culture from specimens of the influenza-like cases in Jiaxing City, and further identified by serological test and reverse-transcription polymerase chain reaction (RT-PCR). Six isolated strains were selected randomly and their sequences of the HA1 genes were analyzed by the software DNAStar. Results The viruses of Yamagata lineage and Victoria lineage were both found to be existent. The 4 strains of selected strains were Victoria lineage, whose homologies of nucleotide acids were 98.6% to 99.7% and those of amino acids were 98.8% to 100.0%, of which,as compared with vaccine strains of 2009-2012, two of them appeared 4 amino acids substitutions at the sites of L58P, N129S, I146V and N171D in HA1 respectively. The 2 strains of selected strains were Yamagata lineage, with the homologies of nucleotide acids and amino acids of 99.4%, and a high similarity to the vaccine strains of 2012 to 2013 recommended by WHO. Conclusion The vaccines recommended by WHO from 2009 to 2012, belonged to Victoria lineage, with a certain protective effect against Victoria lineage strains of influenza B virus, but were unable to provide optimum prevention from Yamagata lineage strains, which also simultaneously prevailed in Jiaxing City during this period.