Background: Influenza is intrinsically characterized by the unpredictable predominance of one or co-circulation of several influenza A subtypes and/or influenza type B lineages in any influenza season. The past decades two antigenically distinct lineages of influenza B viruses have circulated globally since 1985 and have co-circulated since 2001, lineage Victoria and lineage Yamagata.Our aim was to estimate the distribution of the two lineages circulating in Greece and any possible mismatching with vaccine influenza B strains. Methods and materials: We studied 490 laboratory-confirmed influenza B non-severe acute respiratory infection (non-SARI) clinical cases diagnosed in the two National Influenza Reference Laboratories by reverse trancscriptase-PCR from 1/7/2005 to 30/6/2015 and 100 influenza B SARI cases diagnosed from 1/7/2011 to 30/6/2015. The distribution of influenza B lineages Victoria and Yamagata was described and mismatch between circulating lineages and vaccine strains was estimated. Results: Median matching between the circulating influenza B lineages and the vaccine influenza B strains was 19.2% (range: 0–100%) for non-SARI cases during 2005–2015 and 67.6% (range: 41.2–94.1%) for SARI cases during 2011–2015. In two influenza seasons (2005–2006 and 2006–2007) complete mismatch between influenza B non-SARI cases and influenza B vaccine strains was found. We estimated that 5, 12 or 16 laboratory-confirmed SARI cases could have been prevented by quadrivalent influenza vaccine during the 2011–2012 season and 1, 3, or 4 SARI cases during the 2014–2015 season, with a vaccination coverage rate of 70% and a vaccine effectiveness of 20%, 50% or 70%, respectively. Conclusion: Significant co-circulation of lineage Victoria and Yamagata influenza B strains and mismatching with vaccine influenza B strains was found during 2005–2015 in Greece. The wide use of a quadrivalent influenza vaccine instead of a trivalent influenza vaccine will confer additional immunity and therefore protection against influenza B and it is expected to prevent several SARI cases annually. Our findings strongly support the recommendations for using quadrivalent influenza vaccine.