A microscope system includes: a microscope optical system including an ocular lens, the microscope optical system being configured to form an optical image of a sample on an object side of the ocular lens; a processor configured to generate, based on examination information regarding examination to the sample and magnification information regarding a magnification of the microscope optical system, image data of a comparative image for comparison with the optical image; and a superimposition device configured to superimpose, based on the image data generated by the processor, the comparative image onto an image plane on which the optical image is formed.