A microscope system includes an objective lens that focuses, on a specimen, illumination light produced by a light source. An illumination-area switching mechanism is disposed between the objective lens and the specimen and switches an illumination area irradiated with the illumination light focused by the objective lens among a plurality of illumination areas on the specimen that are located outside an objective optical axis of the objective lens. An inner focus lens is disposed on the objective optical axis between the light source and the objective lens and changes a focus position of the objective lens in a direction along the objective optical axis.