To observe and analyze intermolecular interactions such as diffusion and/or binding behaviors of molecules in a sample in a reacting state against optical stimulation, while applying the optical stimulation to a desired region in the sample by irradiating stimulus light. There is provided a fluorescence microscope apparatus comprising: a fluorescence image-capturing optical system; a stimulus light-irradiation optical system which includes a scanner for; a control unit which acquires temporal observation data by repeatedly capturing images using said image-capturing optical system while applying optical stimulation using the stimulus light-irradiation optical system; an analysis unit; and a display unit.