• Influenza B/Victoria and B/Yamagata co-circulate in Taiwan annually. • Influenza B/Yamagata was the major lineage causing intensive care unit (ICU)-admitted influenza with complications. • Compared to patients with B/Victoria infection, ICU-admitted influenza patients with complications infected by B/Yamagata were older. • Compared to B/Victoria-infected ones, ICU-admitted influenza patients with complications infected by B/Yamagata had longer ICU stays. We describe the relative proportions and epidemiological features of influenza B/Victoria and B/Yamagata, using data from nationwide surveillance systems. We collected respiratory samples from outpatients with influenza-like illness (ILI) and intensive care unit (ICU)-admitted patients with complications (pulmonary or neurological complications, myocarditis/pericarditis or invasive bacterial infection) for virus isolation and lineage typing. Demographics, epidemiological features, and vaccination history from ICU-admitted patients with complications were analyzed. From July 2013–June 2017, 21% of 11517 influenza isolates were influenza B. B/Victoria was the predominant circulating strain in 2013–2014, accounted for 56% of all influenza B positive samples and B/Yamagata was predominant in 2014–2017 (82%, 69%, and 85%, respectively). Among all typed viruses, the proportion of B/Yamagata was higher among specimens from ICU-admitted patients with complications (77%, 154/199) than from ILI outpatients (66%, 276/418, p < 0.005). Compared to B/Victoria, B/Yamagata infected ICU-admitted patients with complications were older, median age (71 vs. 59 years, p < 0.05), had longer durations of hospitalization (15 vs. 7.5 days, p < 0.05) and ICU stays (8.5 vs. 5.5 days, p < 0.05). Two lineages of influenza B viruses co-circulate annually in Taiwan. Among ICU-admitted patients with complications, B/Yamagata causes more severe illness than B/Victoria. [ABSTRACT FROM AUTHOR]