A microscope system includes: a stage on which an observation sample is mounted; an objective lens; a driving unit configured to drive the stage or the objective lens to change a distance between the stage and the objective lens; a light source configured to selectively irradiate the observation sample with one of autofocus detection light and excitation light; an irradiation region changing unit configured to change a region in which the observation sample is irradiated with light; a first mirror unit; a second mirror unit; a mirror arrangement unit configured to selectively arrange one of the first mirror unit and the second mirror unit on the optical axis; an imaging unit configured to capture the observation sample; a light intensity calculating unit configured to calculate light intensity; and a controller configured to adjust, based on a reference position, a distance between the observation subject and the objective lens.