A microscope apparatus includes a detection optical system that detects fluorescence produced in a specimen immersed in a medium having a different refractive index from air and accommodated in a container and acquires a fluorescence image. An illumination device focuses excitation light emitted from an excitation-light source, in the form of a plane along a plane intersecting an optical axis of the detection optical system and makes the planar excitation light incident on the specimen in the container. A driving unit moves the specimen in a direction of an optical axis of a cylindrical lens. An illumination control unit adjusts a focal position of the illumination device based on a movement amount of the specimen moved by the driving unit such that an air-equivalent length along an optical path of the excitation light from the illumination device to the optical axis of the detection optical system remains constant.