A biological observation system includes: a light source section generating illumination light including at least first illumination light with a center wavelength from a red region to a near infrared region of a visible region; a light detection section receiving return light emitted from a region to be observed to which the illumination light is applied and outputting an output signal; a signal processing section generating a frequency spectrum signal indicating a frequency spectrum of the return light emitted from the region to be observed according to application of the first illumination light; an image generation section generating an intensity image based on the output signal and generate a frequency spectrum image based on the frequency spectrum signal; and a display control section generating and displaying an observation image of the region to be observed by using the intensity image and the frequency spectrum image.