An endoscope system includes: a light source unit that alternatingly emits first illumination light and second illumination light； an imaging means for generating a first image signal of a subject illuminated by the first illumination light, and generating a second image signal of the subject illuminated by the second illumination light； a first image signal storing means for storing the first image signals； a second image signal storing means for storing the second image signals； an image evaluation value calculating means for calculating at least one of image evaluation values based on the first image signals and image evaluation values based on the second image signals； an image signal selecting means for selecting a first display image signal and selecting a second display image signal based on the image evaluation values； and a displaying means for displaying a first image and a second image that are based on the first display image signal and the second display image signal respectively.
