Trace amounts of water dissolved in minerals affect density, viscosity and melting behaviour of the Earth’s mantle and play an important role in global tectonics, magmatism and volatile cycle. Water concentrations and the ratios of hydrogen isotopes in the mantle give insight into these processes, as well as into the origin of terrestrial water. Here we show the presence of molecular H2 in minerals (omphacites) from eclogites from the Kaapvaal and Siberian cratons. These omphacites contain both high amounts of H2 (70 to 460 wt. ppm) and OH. Furthermore, their ∂D values increase with dehydration, suggesting a positive H isotope fractionation factor between minerals and H2–bearing fluid, contrary to what is expected in case of isotopic exchange between minerals and H2O-fluids. The possibility of incorporation of large quantities of H as H2 in nominally anhydrous minerals implies that the storage capacity of H in the mantle may have been underestimated, and sheds new light on H isotope variations in mantle magmas and minerals.