The image pickup apparatus includes an image sensor having plural pixels each being constituted by a microlens causing light fluxes from mutually different areas in an exit pupil of an image capturing optical system to form two object images and two photoelectric conversion portions photoelectrically converting the two object images, a signal reader performing a first reading operation that adds signals from the two photoelectric conversion portions to read the added signal as a pixel signal and a second reading operation that independently reads the signal from each of the two photoelectric conversion portions as the pixel signal, and a phase difference detector detecting a phase difference between the two object images by using the pixel signal read by the second reading operation. The signal reader performs, when the phase difference is detected, the second reading operation on pixel lines located discretely among plural pixel lines in the image sensor.