The protein-induced chemical structure in calcified organisms is an important factor contributing to their growth, but until now no direct evidence has been reported. Hence, we demonstrate a new analytical technique that combines an FTIR spectrometer and an apertureless-type near-field microscope with high spatial resolution. The complete structural composition of the biomineralized structure of marine organisms has been measured using this technique. The results show that -OH is distributed over the center of the mineral phase of small calcite, which was formed from interactions of matrix proteins.