A biological observation system includes: a light source apparatus configured to supply a first illuminating light including a plurality of wavelength bands, and a second illuminating light including a plurality of wavelength bands that differ from the wavelength bands of the first 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 illuminated by illuminating light at each of a plurality of pixels having different sensitivities, and generate an image pickup signal； a color separation processing portion configured to separate, from an image pickup signal for respective color components generated by the image pickup device, an image pickup signal corresponding to 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 among the plurality of pixels； and a control portion configured to cause different color separation processing to be performed between a case where an image pickup signal inputted to the color separation processing portion is an image pickup signal corresponding to the first illuminating light and a case where an image pickup signal inputted to the color separation processing portion is an image pickup signal corresponding to the second illuminating light.
