Hydrate equilibrium conditions formed from deuterated methane isotopologues (CH3D and CD4) were measured over a temperature range of (273 to 278) K and a pressure range of (2.6 to 4.2) MPa. The phase boundary of CH3D and CD4 hydrates was shifted to higher pressures and lower temperatures than that of the CH4 hydrate. Crystal structure and cage occupancies of gas hydrate crystals formed from CH3D and CD4 were characterized by Raman spectroscopy. The isotope effect of methane hydrates revealed in this study can be used to explain the isotopic fractionation of hydrogen in methane during the formation of clathrate hydrates observed in natural settings, as reported by previous studies.