An endoscope system includes a light source apparatus capable of supplying excitation light for generating fluorescence and reference light in a different wavelength band from the fluorescence, an objective optical system, an optical filter configured to block reflected light of the excitation light, an image pickup section configured to separate, and pick up, light that is emitted through the optical filter into the fluorescence, light in a first wavelength band, and light in a second wavelength band, an observation image generation section configured to generate an observation image by using first to third signals obtained by picking up the fluorescence, the light in the first wavelength band, and the light in the second wavelength band, and a control section configured to cause the first signal to be assigned to a green component of a display apparatus, and to cause a signal having a relatively large signal value, between the second and the third signals, to be assigned to a red component of the display apparatus and a signal having a relatively small signal value to be assigned to a blue component of the display apparatus.
