We present a theoretical model to investigate the potential of 13CH3D and 12CH2D2, the doubly substituted mass-18 isotopologues of methane, as tools for tracking atmospheric methane sources and sinks. We use electronic structure methods to estimate kinetic isotope fractionations associated with the major sink reactions of methane in air (reactions with OH and Cl radicals) and combine literature data with reconnaissance measurements of the relative abundances of 13CH3D and 12CH2D2 to estimate the compositions of the largest atmospheric sources. This model atmospheric budget is investigated with a simplified box model in which we explore both steady state and dynamical (nonsteady state) conditions triggered by changes in emission or sink fluxes. The steady state model predicts that sink reactions will generate a marked (>100‰) clumped isotope excess in atmospheric Δ12CH2D2 relative to the net source composition. 12CH2D2 measurements may thus be useful for tracing both atmospheric source and sink fluxes. The effect of sinks on Δ13CH3D is much less pronounced, indicating that 13CH3D in air will give a more focused picture of the source composition.