To investigate the genetic characteristics of human influenza type B viruses circulating in Chungbuk province, Korea, we tested 510 clinical samples of nasopharyngeal suction from pediatric patients diagnosed with respiratory illness between June 2007 and June 2008. Twelve out of thirty-six isolates were identified as type B influenza virus by RT-PCR and sequencing analysis. Interestingly, genetic characterization of type B viruses isolated in this study revealed that all type B influenza viruses were the Yamagata lineages, a vaccine strains of southern hemisphere during 2007~2008, rather than the Victoria lineage of northern hemisphere during 2007~2008. Furthermore, there were a total of twelve unique mutations (HA: H40Y, D/G230S, V252M and K272R and NA: P3H, P/T/S42Q, N59S) occurred in our type B isolates. These results suggest that relative high prevalence of type B viruses in Korea during 2007~2008 season might be due to the wrong vaccine strains selection. Taken together, the results of this study demonstrate continuous evolutions of human type B viruses by antigenic drift and also highlight the need to closely monitoring of influenza viruses to aid the early detection of potentially pandemic strains as well as underscore the need for new therapeutics.