Abstract: Objective To understand the haemagglutinin genetic characteristics and molecular epidemiological characteristics of influenza B virus in Nanchang, Jiangxi province, in 2011. Methods Totally 25 strains of influenza B virus isolated in Nanchang in 2011 were cultured in MDCK cell. Viral RNA were extracted and HA1 gene were amplified by using RT-PCR. The amplified products were purified and the nucleotide sequences were determined, the results were analyzed by Mega 4.1 software. Results It was found that Yamagata lineage and Victoria lineage virus strains co-circulated in Nanchang in 2011 and the Victoria lineage virus was predominant(84%). Compared with the vaccine strain B/Brisbane/60/2008, there were 8 amino acids substitutions in HA1 fragment of Victoria lineage strains in 2011, in which there was 1 amino acid mutation relating to antigenic sites B. Compared with the vaccine strain B/Wisconsin/1/2010, there were 19 amino acids substitutions in HA1 fragment of Yamagata lineage strains, the mutations of R130K, T165N, Q195R, Q196T were related to antigenic sites A, C and D. Conclusion The circulated Victoria lineage virus was the predominant strain of influenza B virus in Nanchang in 2011, and there was no obvious variation of haemagglutnin in Victoria lineage strains, but in Yamagata lineage strains.