An image pickup element includes a first substrate, a second substrate, first pixels, and second pixels irradiated with light transmitted through the first pixels, and the second pixel includes a first PN junction surface parallel to a light-receiving surface, and a second PN junction surface positioned deeper than the first PN junction surface and parallel to the light-receiving surface, and the second pixel generates a second signal corresponding to light of a second wavelength band from electric charge obtained by the second PN junction surface.