An endoscope apparatus comprises: a light source section configured to emit to a living tissue dispensed with a fluorescent substance, excitation light in a first wavelength band and reference light in a second wavelength band； an excitation light cut filter section that shuts off the excitation light； a color filter section provided with a first filter having relatively high transmittance in a third wavelength band including the wavelength band of the fluorescence emitted from the fluorescent substance, and a second filter having relatively high transmittance in the second wavelength band； an image pickup section that generates an image in accordance with intensity of a return light received when the excitation light and the reference light are simultaneously emitted to the living tissue dispensed with the fluorescent substance； and an image processing unit that acquires a first image obtained by separating a signal component generated upon receiving the fluorescence and a second image obtained by separating a signal component generated upon receiving the reference light respectively, from the respective color components included in the image.
