There is provided a microscope apparatus including: a plurality of objective lenses having different magnifications; an imaging system that receives light, which is generated from a sample and emitted from the objective lens when excitation light is emitted to a sample including a fluorescent material that is activated when irradiated with activation light having a predetermined wavelength and fluoresces to be inactivated when irradiated with excitation light having a different wavelength from the activation light in the activation state and that images the light in a state where an astigmatic difference is given to the image of the sample; and an imaging device that captures the image of the sample from the imaging system. The imaging system includes an astigmatic difference changing device that changes the astigmatic difference according to the depth of focus of the objective lens.