Microscopic in vivo pH imaging system is developed that can capture the luminescent- and color-imaging. The former gives a quantitative measurement of a pH distribution in vivo. The latter captures the structural information that can be overlaid to the pH distribution for correlating the structure of a specimen and its pH distribution. By using a digital color camera, a luminescent image as well as a color image is obtained. The system uses HPTS (8-hydroxypyrene-1,3,6-trisulfonate) as a luminescent pH indicator for the luminescent imaging. Filter units are mounted in the microscope, which extract two luminescent images for using the excitation-ratio method. A ratio of the two images is converted to a pH distribution through a priori pH calibration. An application of the system to epidermal cells of Lactuca Sativa L is shown.