An object of the present invention is to provide a predetermined site luminescence measuring method and a predetermined site luminescence measuring apparatus, which allow for determining whether, when the luminescence from the predetermined site in live samples is measured, a photoprotein is localized at the predetermined site in the same ones as the samples. An predetermined site luminescence measuring apparatus 100 in the present invention is comprised of: a the sample 102 into which a fused fusion gene is introduced, the fusion gene being obtained by fusing a fluorescence-related gene that expresses a fluorescence protein in addition to a targeting base sequence and a luminescence-related gene; a container 103 for storing the sample 102, a stage 104 on which the container 103 is arranged; a luminescent image capturing unit 106 which captures a luminescent image of the sample 102 (the objective lens 106a to the CCD camera 106c, and the imaging lens 106f); a fluorescent image capturing unit 108 which captures a fluorescent image of the sample 102 (the objective lens 108a to shutter 108f); and an the information communication terminal 110.