A photographing apparatus comprising: a first photographing section that includes a first photographing optical system which includes a first focus lens, a first focus lens driving section which moves the first focus lens in an optical axis direction, and a first imaging element which receives subject light obtained by focusing a subject with the first photographing optical system and generates an image signal representing the subject; a second photographing section that includes a second photographing optical system which includes a second focus lens, a second focus lens driving section which moves the second focus lens in an optical axis direction, and a second imaging element which receives subject light obtained by focusing the subject with the second photographing optical system and generates an image signal representing the subject; a focus position determining means that is adapted to instruct the first and second focus lens driving sections to search for focus positions while moving the first and second focus lenses and to stop the first and second focus lenses at the focus positions, respectively; and a deviation storing section that is adapted to store a deviation of the focus position of the second focus lens searched by the focus position determining means from the focus position of the first focus lens searched by the focus position determining means; wherein the focus position determining means is adapted to perform when the deviation is not stored in the deviation storing section, a first focus position determination, to search for the focus position while moving the first focus lens in a predetermined first search area and to stop the first focus lens at the focus position, and for the second photographing optical system, to search for the focus position while moving the second focus lens in a second search area narrower than the first search area including a focus expected position of the second focus lens corresponding to the focus position of the first focus lens and to stop the second focus lens at the focus position, and when the deviation is stored in the deviation storing section, a second focus position determination, for the first photographing optical system, to search for the focus position while moving the first focus lens and to stop the first focus lens at the focus position, and for the second photographing optical system, to move the second focus lens to a position more deviated by the deviation stored in the deviation storing section than a focus position corresponding to the focus position of the first focus lens. a first photographing section that includes a first photographing optical system which includes a first focus lens, a first focus lens driving section which moves the first focus lens in an optical axis direction, and a first imaging element which receives subject light obtained by focusing a subject with the first photographing optical system and generates an image signal representing the subject; a second photographing section that includes a second photographing optical system which includes a second focus lens, a second focus lens driving section which moves the second focus lens in an optical axis direction, and a second imaging element which receives subject light obtained by focusing the subject with the second photographing optical system and generates an image signal representing the subject; a focus position determining means that is adapted to instruct the first and second focus lens driving sections to search for focus positions while moving the first and second focus lenses and to stop the first and second focus lenses at the focus positions, respectively; and a deviation storing section that is adapted to store a deviation of the focus position of the second focus lens searched by the focus position determining means from the focus position of the first focus lens searched by the focus position determining means; wherein the focus position determining means is adapted to perform when the deviation is not stored in the deviation storing section, a first focus position determination, to search for the focus position while moving the first focus lens in a predetermined first search area and to stop the first focus lens at the focus position, and for the second photographing optical system, to search for the focus position while moving the second focus lens in a second search area narrower than the first search area including a focus expected position of the second focus lens corresponding to the focus position of the first focus lens and to stop the second focus lens at the focus position, and when the deviation is stored in the deviation storing section, a second focus position determination, for the first photographing optical system, to search for the focus position while moving the first focus lens and to stop the first focus lens at the focus position, and for the second photographing optical system, to move the second focus lens to a position more deviated by the deviation stored in the deviation storing section than a focus position corresponding to the focus position of the first focus lens.