A fundus photographing apparatus includes: a photographing unit including a fundus illumination optical system to illuminate a fundus of a patient's eye and a fundus photographing optical system having a light receiving element to obtain a fundus image of the illuminated eye; and an alignment unit to position the photographing unit with the eye based on a predetermined alignment reference position. The alignment unit includes: an extracting part to extract, by image processing, an image region formed by reflection light from a portion other than the fundus from the fundus image obtained by the fundus photographing optical system; a gravity center calculating part to determine, by arithmetic processing, a gravity center position of the extracted image region; and a control part to perform alignment control of the photographing unit with the eye based on the calculated gravity center position and the alignment reference position.