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Both hydrogen and methane are consistently discharged in large quantities in hydrothermal fluids issued from ultramafic-hosted hydrothermal fields discovered along the Mid-Atlantic Ridge. Considering the vast number of these fields discovered or inferred, hydrothermal fluxes represent a significant input of H2 and CH4 to the ocean. Although there are lines of evidence of their abiogenic formation from stable C and H isotope results, laboratory experiments, and thermodynamic data, neither their origin nor the reaction pathways generating these gases have been fully constrained yet. Organic compounds detected in the fluids may also be derived from abiotic reactions. Although thermodynamics are favorable and extensive experimental work has been done on Fischer-Tropsch-type reactions, for instance, nothing is clear yet about their origin and formation mechanism from actual data. Since chemolithotrophic microbial communities commonly colonize hydrothermal vents, biogenic and thermogenic processes are likely to contribute to the production of H2, CH4, and other organic compounds. There seems to be a consensus toward a mixed origin (both sources and processes) that is consistent with the ambiguous nature of the isotopic data. But the question that remains is, to what proportions? More systematic experiments as well as integrated geochemical approaches are needed to disentangle hydrothermal geochemistry. This understanding is of prime importance considering the implications of hydrothermal H2, CH4, and organic compounds for the ocean global budget, global cycles, and the origin of life.