Abstract: Objective To understand the molecular epidemiological characteristics of hemagglutinin (HA) and neuraminidase (NA) of influenza B virus isolated in Ningbo, Zhejiang province, during 2003-2014. Methods Respiratory specimens were collected from local patients with influenza like illness for influenza virus isolation and identification. The sequencing of HA gene and NA gene of influenza B virus isolated at different times were performed. The phylogenetic and genetic diversity analyses were conducted by using bioinformation software. Results The mutations in amino acid sequence of HA and NA genes were observed in influenza B viruses Victoria lineage and Yamagata lineage isolated in Ningbo from 2003 to 2014. The obvious mutation was for Victoria lineage strains in 2005 and 2009 and Yamagata lineage strains in 2007 and 2010. The mutation of NA gene occurred along with the mutation of HA gene, but sometimes the mutation of NA gene was more obvious than that of HA gene. The influenza B virus isolated during 2013-2014 seemed to be reassortant to have Victoria lineage NA and Yamagata lineage HA. Conclusion Both the mutation of NA gene and the mutation of HA gene might occur for influenza B viruses Victoria lineage and Yamagata lineage, and the mutation of NA gene is more rapid. The influenza B virus isolated in Ningbo during 2013-2014 was reassortant to have Victoria lineage NA and Yamagata lineage HA.