A microscope system, comprising: a microscope adapted to observe a specimen by switching a plurality of observing methods, the plurality of observing methods comprising fluorescent observing methods in which fluorescent observation is performed for different wavelengths; selection instruction means adapted to receive a selection instruction to select one of the fluorescent observing methods as a main method; image pickup means adapted to capture fluorescent images of the specimen based on the selected main method; an image record unit adapted to store the captured fluorescent images; superposition means (S706-S707) adapted to superpose images; display control means adapted to control display of the superposed images; superposition release means adapted to release a superposition state of the superposed image; and detection means adapted to detect an operation of the microscope which generates a change of an observation environment of shooting the specimen, wherein said operation relates to at least one of moving a stage loaded with the specimen, changing a magnification, and focusing; characterized in that the selection instruction means are adapted to receive a selection instruction to select at least one of the other fluorescent observing methods as a non-main method; and the superposition means (S706-S707) are adapted to superpose at least one stored fluorescent observation image based on a selected non-main method on a live fluorescent observation image based on the selected main method; and the superposition release means are adapted to release a superposition state of the superposed image based on a detection result of the detection means; and in that the display control means are adapted to control display of solely the live fluorescent image based on the selected main method upon release of the superposition state. a microscope adapted to observe a specimen by switching a plurality of observing methods, the plurality of observing methods comprising fluorescent observing methods in which fluorescent observation is performed for different wavelengths; selection instruction means adapted to receive a selection instruction to select one of the fluorescent observing methods as a main method; image pickup means adapted to capture fluorescent images of the specimen based on the selected main method; an image record unit adapted to store the captured fluorescent images; superposition means (S706-S707) adapted to superpose images; display control means adapted to control display of the superposed images; superposition release means adapted to release a superposition state of the superposed image; and detection means adapted to detect an operation of the microscope which generates a change of an observation environment of shooting the specimen, wherein said operation relates to at least one of moving a stage loaded with the specimen, changing a magnification, and focusing; characterized in that the selection instruction means are adapted to receive a selection instruction to select at least one of the other fluorescent observing methods as a non-main method; and the superposition means (S706-S707) are adapted to superpose at least one stored fluorescent observation image based on a selected non-main method on a live fluorescent observation image based on the selected main method; and the superposition release means are adapted to release a superposition state of the superposed image based on a detection result of the detection means; and in that the display control means are adapted to control display of solely the live fluorescent image based on the selected main method upon release of the superposition state.