A multi-excitation fluorometer, the Multi-Exciter (MEX), is designed to identify phytoplankton composition based on the fluorescence provided by nine different excitation wavelengths. The phytoplankton community structure was monitored using MEX off the coast of eastern Hokkaido, Japan, from 2019 to 2021, encompassing the period of an outbreak of the harmful dinoflagellate Karenia spp. (Karenia selliformis, K. mikimotoi, and K. longicanalis) in autumn 2021. MEX could distinguish the vertical structure of spring diatom blooms but not that of dinoflagellate blooms in October 2021. This is possibly because MEX identified peridinin-type dinoflagellates, whereas Karenia spp. lacked peridinin. The Karenia index was defined based on the similarities in fluorescence properties (36 combinations of the ratio of fluorescence values obtained using MEX) of representative Karenia bloom water, aiming to overcome this misidentification. High Karenia indices were observed at depths of 1 m-20 m in October 2021. This implied that Karenia spp. were distributed at depths of < 20 m during their blooms, and MEX detected Karenia blooms with their vertical structure. No Karenia spp. were observed using microscopy in May 2021; however, high Karenia indices were observed in the subsurface. Hence, the fluorometric approach is a simple and rapid method for identifying distinguishing events in the phytoplankton community when combined with sporadic microscopic observations.