An imaging apparatus includes: a first illumination unit to apply visible light to a subject having a fluorescent substance； a second illumination unit to apply excitation light to the subject so that fluorescence is generated from the fluorescent substance； an optical filter unit to cause the visible light and the fluorescence to pass therethrough, and shield the excitation light； an imaging unit including imaging elements to generate image signals, and an output unit to read the image signals from the imaging elements and output image information； an optical element to divide the visible light into component light beams, cause the divided light beams to be incident on the imaging elements, and cause the fluorescence to be incident on at least one imaging element； and a control means for alternately applying the visible light and the excitation light and alternately outputting image information of the visible light and the fluorescence.
