Molecular hydrogen (H₂) is an important metabolite cycled by microorganisms within the human gastrointestinal tract (GIT) with key roles in human nutrition and health. H2 is produced during fermentation by various bacteria and consumed as an energy source by other bacteria, including acetogens, methanogens, and sulfate reducers. H₂ has traditionally been used as an indicator of gut dysbiosis through breath tests and the disruption of H₂ cycling is associated with colorectal cancer, IBD and other GI tract disorders. Despite strong links to human health, the microorganisms, enzymes, and pathways responsible for gastrointestinal H2 production remain unresolved. Here we show that a previously uncharacterised enzyme, the group B [FeFe]-hydrogenases encoded by all four dominant gut phyla, primarily mediates fermentative H2 production in gut microbiota. Leveraging a vast dataset of 402 stool and biopsy metagenomes, 78 metatranscriptomes, and 801 gut bacterial isolate genomes, we show that the genes for this enzyme are abundant, highly expressed, and widely distributed in the human GIT. Based on transcriptomic and gas chromatography analysis of 16 taxonomically diverse gut isolates, the group B [FeFe]-hydrogenases mediates rapid H2 production during fermentative growth. Furthermore, Bacteroides, a genus previously unknown to be hydrogenogenic, are dominant H₂ producers in this environment. In addition, biochemical characterisation confirmed that the group B [FeFe]-hydrogenase is catalytically active and binds a diiron centre. This combination of culture-dependent and culture-independent analysis provides new insights into how H₂ is produced within the human GI tract, and identifies the key groups involved, enhancing our ever-growing understanding of the impacts of the gut microbiota on human health.