Provided is a microscope system including: a plurality of objective lenses that are selectively used to collect fluorescence from a specimen; a detecting unit that obtains image information of the specimen on the basis of the fluorescence collected by the objective lens; and an adjustment unit that adjusts the observation range of the specimen S and that divides the observation range into one or more observation regions corresponding to a capture range captured by the detecting unit, wherein the adjustment unit calculates an observation magnification at which the entire well is included in the observation range, the number of observation regions is minimized, and the resolution becomes the highest, on the basis of information about the size of the well in a multi-plate for accommodating the specimen and information about an objective magnification of the objective lens, and adjusts the observation range on the basis of the calculated observation magnification.