An image pickup element includes a pixel matrix, a pupil dividing portion, and a shielding portion. Pixels in the pixel matrix include a photoelectric conversion portion, and are arranged in units of a matrix of a predetermined number of the pixels. The pupil dividing portion is arranged on a side of a light receiving surface of the photoelectric conversion portion of each pixel to divide a pupil region. The shielding portion arranged between the pupil dividing portion and the photoelectric conversion portion shields a predetermined region of the light receiving surface of the photoelectric conversion portion. The predetermined region of each pixel corresponds to any one of the divided pupil regions obtained when the pupil region is divided by the pupil dividing portion. A proportion of the predetermined region is smaller than a proportion of a region not-shielded by the shielding portion in the light receiving surface.