The microscopic mechanism of the proton diffusion in protonic conductors, Sc-doped SrTiO3 and Y-doped SrCeO3, is studied by a first-principles molecular-dynamics simulation. It is found that the proton forms an O-H bond with the neighboring O ion, and that the frequency of the O-H stretching vibration depends on the position of the proton in these crystals. It is shown that the position dependence of the O-H stretching vibration is induced by the presence of doped acceptor ions.