An influenza B outbreak occurred in Taiwan in 2004 to 2005, during which both Victoria and Yamagata lineages co-circulated. This study examined 36 influenza B viral genomes isolated during the outbreak to reveal their reassortment patterns. According to the isolate groupings in phylogenetic analysis, we were able to categorize those 36 isolates as either of Victoria and Yamagata lineage for all 8 influenza B genomic segments, except for the NS gene, in which clade A and B existed. Based on these groupings, three genome patterns clearly emerged, namely, pattern I (Vic+Vic+Ya+Vic+Ya+Ya+Ya+A from segments 1-8), pattern II (Ya+Ya+Ya+Ya+Ya+Ya+Ya+B), and pattern III (Ya+Ya+Ya+Ya+Ya+Ya+Ya+A). According to the timeline of those isolates under investigation, it appears that patterns I and II viruses could have generated pattern III via reassortment of the NS gene. On the other hand, a genome-wide comparison of all six pattern III Taiwanese viruses with 37 international influenza B viral genomes showed that two international strains - B/Oslo/71/04 and B/England/23/04, were consistently clustered with those pattern III viruses isolated in Taiwan in 2004-2005, suggesting that Taiwanese pattern III viruses might also have been possibly imported due to their matching genomic composition.