Cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (H2) that is emitted by the termites; however, little is known about the physiology and biochemistry of H2 production from cellulose in the gut symbiotic protists due to their formidable unculturability. In order to understand the molecular basis for H2 production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (Fe hydrogenases) in Pseudotrichonympha grassii, a large cellulolytic symbiont in the phylum Parabasalia, in the gut of the termite Coptotermes formosanus. The two Fe hydrogenases were phylogenetically distinct and had different N-terminal accessory domains. The long-form protein represented a phylogenetic lineage unique among eukaryotic Fe hydrogenases, whereas the short form was monophyletic with those of other parabasalids. Active recombinant enzyme forms of these two Fe hydrogenases were successfully obtained without the specific auxiliary maturases. Although they differed in their extent of specific activity and optimal pH, both enzymes preferentially catalyzed H2 evolution rather than H2 uptake. H2 evolution, at least that associated with the short-form enzyme, was still active even under high hydrogen partial pressure. H2 evolution activity was detected in the hydrogenosomal fraction of P. grassii cells; however, the vigorous H2 uptake activity of the endosymbiotic bacteria compensated for the strong H2 evolution activity of the host protists. The results suggest that termite gut symbionts are a rich reservoir of novel Fe hydrogenases whose properties are adapted to the gut environment and that the potential of H2 production in termite guts has been largely underestimated.