An endoscope apparatus includes an illuminating section capable of irradiating a subject with a light in a first wavelength band and light in a second wavelength band, an image processing section including a color filter configured by a plurality of filters, the image processing section generating, from two image pickup signals respectively generated in a first pixel and a second pixel that respectively receive light in a predetermined wavelength band and light in a wavelength band different from the predetermined wavelength band among return lights from the subject, first and second image signals, a control section that determines whether the two image pickup signals can be separated into the first and second image signals, and an illumination control section that performs irradiation in a time division manner or simultaneous irradiation according to a determination result whether the separation is possible or not.