A recently introduced fluorescence based real-time bioaerosol instrument, BioScout, and an ultraviolet aerodynamic particle sizer (UVAPS) were used to study fluorescent bioaerosol particles (FBAP) in the Helsinki metropolitan area, Finland, during winter and summer. Two FBAP modes at 0.5–1.5 µm (fine) and 1.5–5 µm (coarse) were detected during the summer, whereas the fine mode dominated in the winter. The concentration and proportion of the coarse FBAP was high in summer (0.028 #/cm3, 23%) and low in winter (0.010 #/cm3, 6%). Snow cover and low biological activity were assumed to be the main reasons for the low coarse FBAP concentration in the wintertime. Both the fine and the coarse FBAP fraction typically increased at nighttime during the summer. Correlations between the BioScout and the UVAPS were high with the coarse (R = 0.83) and fine (R = 0.92) FBAP. The BioScout showed 2.6 and 9.7 times higher detection efficiencies for the coarse and fine FBAP, respectively, compared to the UVAPS. A long-range transport episode of particles from Eastern Europe increased the fine FBAP concentration by over two orders of magnitude compared to the clean period in the winter, but these FBAP probably also included fluorescent non-biological particles. Correlation analysis indicates that local combustion sources did not generate fluorescent non-biological particles that can disturb fine FBAP counting. The results provide information that can be used to estimate health risks and climatic relevance of bioaerosols in the urban environment.