Methyl groups are found in numerous biogenic and synthetic materials including geologically preserved materials such as wood. The carbon and hydrogen isotope compositions of methyl groups are used as tracers in biogeochemical cycles, as paleothermometers, and to determine the hydrogen isotopic composition of ancient rain. Here we present analyses of resolved 13C–D (13CH2D) and D–D (12CHD2) clumped isotope compositions of methyl groups as new variables for the study of methyl groups in the present and past. We first present chemical methods to extract, purify, and derivatize methyl groups from methoxyl (R–O–CH3) groups as CH3F and CH3Cl, and high-resolution mass spectrometric techniques to determine the clumped isotope compositions of these species. We achieve precisions for 13C–D clumping of ±0.25‰ and D–D clumping of ±2.5‰. We anchor our clumped isotopic measurements to a thermodynamic reference frame by first calculating the theoretical temperature dependences of 13C–D and D–D clumping in CH3Cl, then placing our measurements onto this reference frame through experimental internal isotopic equilibration of CH3Cl at 200 °C. Finally, we provide and analyze an initial dataset of clumped 13C–D and D–D compositions of methyl groups from various commercial/synthetic monomers and environmental woods. We observe ranges in clumped isotope compositions of ∼11‰ in 13C–D and ∼48‰ in D–D, and systematic differences within these ranges between methyl groups from commercial monomers and wood. Specifically, commercial clumped 13C–D compositions are between 0 and 3‰, which correspond to apparent equilibrium temperatures between 170 °C and the infinite temperature limit. In contrast, the clumped 13C–D compositions of wood methoxyl groups are distinctively high (9.50–11.25‰) and 3–6‰ higher than would be expected if formed in internal isotopic equilibrium at Earth-surface temperatures. Commercial/synthetic methyl and wood methoxyl clumped D–D compositions are also distinct: −5 to +13‰ in commercial monomers vs. −35 to −8‰ in wood—such negative values cannot result from formation in isotopic equilibrium and require kinetic processes to have occurred. These results indicate that wood methoxyl groups are formed out of isotopic equilibrium and that clumped isotope compositions of methyl groups may be useful tracers of methyl group sources and sinks in the environment. For instance, isotopic clumping in methyl groups may be useful for understanding controls on isotopic clumping in methane produced by methylotrophic methanogens.