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We present a method for measuring the clumped isotope composition of molecular hydrogen (H 2) using a high-resolution mass spectrometer, the Thermo 253 Ultra, improved to address subtle artifacts arising from instrument baselines and non-linear responses. We also present methods for purification and concentration of H 2 from natural and experimental samples, tailored to this measurement. We document the accuracy of the method through comparison to established methods for the determination of δ D values, and through measurements of H 2 gases of widely varying D content that were driven to isotopic equilibrium with respect to their distributions of isotopologues by heating in the presence of a catalyst. Experimental reproducibility of δ D and ΔDD values over months averages ±0.5 and ± 6.9 ‰, respectively (1σ) — both small fractions of common natural variations. We explore methods of gas purification and handling, and show that preferred methods result in low (0–4 ‰) changes in δ D and undetectable changes in ΔDD. Our methods and data processing procedures were further tested by comparing measurements of mixtures of H 2 gases that varied widely in δ D and ∆DD with a model describing proportions of isotopologues in such mixtures. Application of these methods to H 2 that is residual to laboratory consumption by cultured methanogens shows that metabolic 'back reaction' (metabolic production of H 2 from water-derived protons during net H 2 consumption) is responsible for driving the ΔDD value of residual H 2 toward equilibrium at environmental temperatures. Finally, we report the first measurements of the clumped isotope composition of molecular hydrogen in natural geological samples collected from high and low temperature submarine hydrothermal vents (Lost city, Rainbow, Ashadze) and an intracontinental natural reservoir in Mali; initial findings suggest that ∆DD of H 2 generally records temperatures of fluid venting or long-term storage, even in cases where the δ D of H 2 has not equilibrated with water at those temperatures. This study establishes the first clumped isotope systematics of molecular hydrogen based on both experimental and natural samples, including key processes in the biogeochemical cycle of H 2. • First clumped isotope measurements on natural H 2 samples • Method improved to correct for instrument baselines and non-linearity issues. • ∆DD generally records temperatures of fluid venting or long-term storage. • Cultured hydrogenotrophic methanogens drive the ΔDD value of residual H 2 toward equilibrium at environmental temperatures. [ABSTRACT FROM AUTHOR]