A fluorescence observation apparatus according to the present invention includes a light source section that can emit a plurality of excitation light beams of different wavelength bands and select excitation light beams to be emitted to an object where there are a first fluorescent substance and a second fluorescent substance from among the plurality of excitation light beams, a variable filter section that selectively allows at least part of the wavelength band of returning light from the object to pass, a photo-detecting section that detects the light that has passed through the variable filter section, a calculation processing section that carries out calculations to determine a wavelength band of the excitation light emitted from the light source section and a transmission wavelength band in the variable filter section based on intensity characteristics of the plurality of excitation light beams, fluorescence characteristics of the first fluorescent substance and fluorescence characteristics of the second fluorescent substance and a control section that performs control of causing the light source section to interlock with the variable filter section based on the calculation result of the calculation processing section.
