Abstract: Objective To understand the epidemiological characteristics of influenza B and the antigenic and genetic characteristics of influenza B virus in the mainland of China during 2012-2013. Methods The antigenic characteristics of influenza B virus was analyzed with reference ferret anti-sera. The nucleotide sequences of the influenza B viruses were determined by Sanger dideoxy sequencing. The phylogenetic trees were constructed by neighbor-jointing method, the genetic characteristics were determined and compared the circulating influenza B virus with current vaccine strains. Results During 2012-2013 influenza season influenza B virus accounted for 9.93% of total influenza viruses detected, the activity of B Victoria lineage virus were stronger than B Yamagata lineage virus. Most B Victoria lineage viruses had close antigenic relation with the vaccine strain B/Brisbane/60/2008(83.5%)recommended by WHO in previous year and the representative circulating strain B/Chongqing-Yuzhong/1384/2010(94.7%) in the mainland of China. The majority of B Yamagata lineage viruses had closely antigenic relation with WHO recommended vaccine strain B/Wisconsin/01/2010(99.3%) and WHO vaccine seed B/Hubei-Wujiagang/158/2009(98.0%); phylogenetic analysis on B Victoria lineage viruses indicated that one strain had intra-clade reassortants between HA and NA gene. One of the B Yamagata lineage viruses, B/Sichuan-Gaoxin/1110/2012,was confirmed to be an intra-lineage reassortant with NA gene from B Victoria lineage. Conclusion The activity of B Victoria lineage virus was stronger than Yamagata lineage virus in the mainland of China during 2012-2013 influenza season, but only Yamagata lineage virus was included in the WHO recommended trivalent influenza vaccine for this period, which could not provide protection to B Victoria lineage virus infection.