An endoscope system includes an image pickup section that picks up, light included in return light generated according to radiation of excitation light, and reference light, the return light including the fluorescence, light in a first wavelength band, and light in a second wavelength band； an observation image generation section that generates an observation image using first through third image signals obtained by picking up the return light； and a control section that controls the observation image generation section such that the observation image is generated, by causing the first image signal to be assigned to a green component, and by causing one image signal having a relatively large signal value, between the second image signal and the third image signal, to be assigned to a red component and another image signal having a relatively small signal value to be assigned to a blue component and the green component.
