A microscope system includes a transmission illumination optical system having a light source and a condenser lens; a first dry objective having a magnification of from 20 or higher to 40 or lower and capable of viewing by at least one of a differential interference viewing method and a modulation contrast viewing method; and a second dry objective having a magnification of from 60 or higher to 100 or lower and capable of viewing by a differential interference viewing method; the first objective and the second objective being exchangeable.