A biological observation system includes: a light source apparatus configured to supply a first illuminating light, and a second illuminating light, while switching between the first illuminating light and the second illuminating light； an image pickup device configured to receive light from an object at each of a plurality of pixels having different sensitivities, and picks up an image； a color separation processing portion configured to separate, from respective color components, a color component obtained when an image of light of a predetermined wavelength band is picked up by a pixel having the greatest sensitivity to the light in the predetermined wavelength band； and a control portion configured to cause different processing to be performed between a case where an inputted image pickup signal corresponds to the first illuminating light and a case where an inputted image pickup signal corresponds to the second illuminating light.
