Influenza B virus remains a major cause of respiratory diseases worldwide. Because of limited epidemiological and genetic data, the local and global transmission patterns of influenza B virus are not fully understood. Here we report the molecular and phylogenetic characterization of 163 influenza B virus isolates from pediatric inpatients with influenza-like illness in the winter of 2011-2012 in South Korea. Analysis of haemagglutinin and neuraminidase genes of the influenza B isolates revealed that both B/Victoria (62?%) and B/Yamagata lineages (38?%) co-circulated during that influenza season, and a considerable number of the isolates carried several amino acid substitutions in the four major antigenic epitopes of their haemagglutinin protein.