An image pickup apparatus includes: a pixel portion where pixels of a plurality of colors are arranged in a first direction and a second direction as repetition of a basic array, and an arbitrary pixel is divided into a plurality of divided pixels in the first direction; a mixing portion configured to generate processed pixel signals from image data generated by all divided pixels existing in the pixel portion by performing pixel reduction of a plurality of divided pixel signals related to a same color and a same division position; and a managing/instructing portion configured to, in a case of prioritizing phase difference detection, control the pixel reduction by the mixing portion so that the processed pixel signals are not arranged at regular intervals in the second direction.