A microscope apparatus comprising: an objective lens that is adapted to irradiate a sample with illumination light emitted from a light source and concentrate reflected light which reflects from the sample; an image construction unit that is adapted to detect the reflected light concentrated by the objective lens and construct an image of the sample; an intensity adjustment unit capable of adjusting an intensity of the illumination light to the sample through the objective lens; a light focusing position change unit capable of changing a light focusing position in a direction that crosses an optical axis of the illumination light at a pupil position of the objective lens; a storage unit that is adapted to store, for each observation method which corresponds to a respective light focusing position of the illumination light concentrated on the pupil position of the objective lens, a predetermined intensity of the illumination light to be adjusted by the intensity adjustment unit, and the light focusing position of the illumination light to be targeted by the light focusing position change unit; an observation method switching unit capable of switching the observation method between a Total Internal Reflection Fluorescence, TIRF, observation method and an epifluorescence observation method; and a control unit that is adapted to read out the predetermined intensity of the illumination light and the light focusing position of the illumination light which are stored in the storage unit according to the observation method to be applied by the observation method switching unit, to control an adjustment of the intensity of the illumination light by the intensity adjustment unit to adjust the excitation light to have an appropriate intensity for the observation method to be applied by the observation method switching unit, and to change of the light focusing position of the illumination light by the light focusing position change unit, wherein controlling the adjustment of the intensity of the illumination light by the intensity adjustment unit and the change of the light focusing position of the illumination light by the light focusing position change unit is based on a synchronization signal synchronized with a frame signal for constructing the image which is output by the image construction unit, wherein the intensity adjustment unit is a filter device including a plurality of switchable neutral density filters having mutually different transmittances of the illumination light. an objective lens that is adapted to irradiate a sample with illumination light emitted from a light source and concentrate reflected light which reflects from the sample; an image construction unit that is adapted to detect the reflected light concentrated by the objective lens and construct an image of the sample; an intensity adjustment unit capable of adjusting an intensity of the illumination light to the sample through the objective lens; a light focusing position change unit capable of changing a light focusing position in a direction that crosses an optical axis of the illumination light at a pupil position of the objective lens; a storage unit that is adapted to store, for each observation method which corresponds to a respective light focusing position of the illumination light concentrated on the pupil position of the objective lens, a predetermined intensity of the illumination light to be adjusted by the intensity adjustment unit, and the light focusing position of the illumination light to be targeted by the light focusing position change unit; an observation method switching unit capable of switching the observation method between a Total Internal Reflection Fluorescence, TIRF, observation method and an epifluorescence observation method; and a control unit that is adapted to read out the predetermined intensity of the illumination light and the light focusing position of the illumination light which are stored in the storage unit according to the observation method to be applied by the observation method switching unit, to control an adjustment of the intensity of the illumination light by the intensity adjustment unit to adjust the excitation light to have an appropriate intensity for the observation method to be applied by the observation method switching unit, and to change of the light focusing position of the illumination light by the light focusing position change unit, wherein controlling the adjustment of the intensity of the illumination light by the intensity adjustment unit and the change of the light focusing position of the illumination light by the light focusing position change unit is based on a synchronization signal synchronized with a frame signal for constructing the image which is output by the image construction unit, wherein the intensity adjustment unit is a filter device including a plurality of switchable neutral density filters having mutually different transmittances of the illumination light.