A fundus photographing apparatus has an optical system including a movable focusing lens and photographing a fundus, an optical system photo-receiving by a first image pickup element a target from an alignment target projection optical system and detect an alignment state of the photographing optical system with respect to an eye based on a result by the first element, a detection optical system photo-receiving by a second image pickup element a target from a focus target projection optical system and detect a focus state adjusted by moving the lens based on a photo-receiving result by the second element, a unit controlling a light source to successively emit flash light at predetermined intervals in a predetermined period to perform fluorescent photographing, and a unit controlling movement of the photographing optical system with respect to the eye based on a result by the alignment detection optical system during the predetermined period.