A method of manufacturing an imaging apparatus includes: preparing a substrate comprising a wafer and a silicon layer arranged on the wafer, the wafer including a first semiconductor region made of single crystal silicon with an oxygen concentration not less than 2×1016 atoms/cm3 and not greater than 4×1017 atoms/cm3, the silicon layer including a second semiconductor region made of single crystal silicon with an oxygen concentration lower than the oxygen concentration in the first semiconductor region; annealing the substrate in an atmosphere containing oxygen and setting the oxygen concentration in the second semiconductor region within the range not less than 2×1016 atoms/cm3 and not greater than 4×1017 atoms/cm3; and forming a photoelectric conversion element in the second semiconductor region after the annealing.