An imaging apparatus includes: a first and second optical systems that focus and emit incident light, a transparent wavelength, and a focal length of them being different from each other; an imaging unit that includes a first region on which the light emitted from the first optical system is incident and a second region on which the light emitted from the second optical system is incident, can output, as pixel information, an electric signal after photoelectric conversion from pixels arbitrarily set as read targets; a setting unit that can arbitrarily set the read targets in at least one of the first region and the second region; a reading unit that reads the pixel information from the read targets; a control unit that changes the read targets according to an acquisition target image; and an image processing unit that generates the acquisition target image.