Provided is a microscope system including: a stage on which a sample is placed and that is movable in a direction orthogonal to an observation optical axis; a detecting unit that detects a position of the stage; an imaging unit that acquires an image of the sample on the stage; an image generating unit that generates an overlapped image by overlapping the acquired image with the position of the stage; a searching unit that searches for a position of the acquired image in the generated overlapped image; and a control unit that performs control including causing the image generating unit to stop the overlapping process and causing the searching unit to execute the position search when detection by the detecting unit fails, and causing the image generating unit to resume the overlapping process starting from a search position of the searching unit when the search is successful.