A microscope apparatus (100, 200) for stochastic optical reconstruction microscopy using a three-dimensional method comprising: an illumination system having a first laser light source configured to emit activation light for activating a fluorescent material and a second laser light source configured to emit excitation light for making the activated fluorescent material emit light; a control unit configured to control a sample to be irradiated with the activation light and the excitation light from the first and second laser light sources (41a, 41b), respectively; an objective lens unit comprising a plurality of objective lenses (12a, 12b) having different magnifications; an imaging system having a cylindrical lens unit (50, 150) including at least one cylindrical lens (101, 102, 201, 202, 203, 204, 205), the imaging system being configured to receive fluorescence, which is emitted from a sample including the fluorescent material, through a selected objective lens of the plurality of objective lenses thereby to form an image of the sample to which an astigmatic difference is given by the imaging system; and an imaging device that is configured to capture the image of the sample from the imaging system which is formed on the imaging device, characterised in that the cylindrical lens unit (50, 150) comprises a plurality of cylindrical lenses (101, 102, 201, 202, 203, 204, 205) having different focal lengths as an astigmatic difference changing device configured to change the astigmatic difference given by the imaging system by changing a cylindrical lens of the plurality of cylindrical lenses (101, 102, 201, 202, 203, 204, 205) which is inserted into an optical path of the imaging system according to a depth of focus of the selected objective lens. an illumination system having a first laser light source configured to emit activation light for activating a fluorescent material and a second laser light source configured to emit excitation light for making the activated fluorescent material emit light; a control unit configured to control a sample to be irradiated with the activation light and the excitation light from the first and second laser light sources (41a, 41b), respectively; an objective lens unit comprising a plurality of objective lenses (12a, 12b) having different magnifications; an imaging system having a cylindrical lens unit (50, 150) including at least one cylindrical lens (101, 102, 201, 202, 203, 204, 205), the imaging system being configured to receive fluorescence, which is emitted from a sample including the fluorescent material, through a selected objective lens of the plurality of objective lenses thereby to form an image of the sample to which an astigmatic difference is given by the imaging system; and an imaging device that is configured to capture the image of the sample from the imaging system which is formed on the imaging device, characterised in that the cylindrical lens unit (50, 150) comprises a plurality of cylindrical lenses (101, 102, 201, 202, 203, 204, 205) having different focal lengths as an astigmatic difference changing device configured to change the astigmatic difference given by the imaging system by changing a cylindrical lens of the plurality of cylindrical lenses (101, 102, 201, 202, 203, 204, 205) which is inserted into an optical path of the imaging system according to a depth of focus of the selected objective lens.