Permeation behavior of gas molecules in ultramicropore was investigated by using molecular sieving carbon membranes. Hydrogen and hydrogen isotope (deuterium), which have the same molecular size but different mass, were used in order to discuss the diffusion mechanism. Although the temperature dependence of permeation coefficient apparently obeyed the Knudsen diffusion in the membranes which have wider ultramicropores, the deviation of the separation factor of hydrogen and deuterium from the theoretical value suggested coexistence of the other diffusion mechanism. With decreasing ultramicropore size, the permeation behavior of hydrogen deviated from Knudsen diffusion, indicating surface diffusion dominantly occurred. The stronger interaction of deuterium in ultramicropores was shown by the difference of activation energy of surface diffusion between hydrogen and deuterium. Apparent solubility factor, assuming surface diffusion, clearly showed that the deuterium is considerably adsorbed in ultramicropores more than hydrogen even at ambient temperatures.