Stable hydrogen isotope systematics among H2, H2O, and CH4 during hydrogenotrophic methanogenesis were investigated by growing a thermophilic methanogen, Methanothermobacter thermautotrophicus strain ΔH, in batch cultures spiked with deuterium-labeled H2 and/or H2O. The hydrogen isotope ratio of the product, CH4, reflected not only the isotope ratio of the H2O in the medium but also that of the substrate, H2. The D/H ratios of the CH4 were highest during the early phase of growth, and the growth-phase-dependent changes were greatest in the deuterium-enriched H2 cultures. The hydrogen isotope systematics among H2, H2O, and CH4 during growth of the methanogen could be described with the following equations: δDCH4=a×δDH2O+b×δDH2-ca=0.71-0.55×b0.17⩽b⩽0.38c=1000×(a+b-1) The greatest effect of δDH2 on δDCH4 (b=0.38) was observed during the earliest phase of growth. In contrast to this study, the possible disappearance of the effect (b=0) has been suggested in a previous study (Valentine et al., 2004a) in which Methanothermobacter marburgensis was cultured and hydrogen isotope systematics during growth was monitored, as was the case in this study. The close phylogenetic relationship between M. thermautotrophicus and M. marburgensis, which likely have similar biochemical pathways, suggests a possibly broad range of the b value, 0–0.38. To explain the observed hydrogen isotope systematics, two cellular mechanisms were proposed. One is that the hydrogen atoms of both H2 and H2O are directly incorporated into the product, CH4. The other is that all four hydrogen atoms in the product, CH4, are derived from intracellular H2O, which consists of a mixture of medium-derived pristine H2O and isotopically distinct H2O derived from methanogenic H2 oxidation. Although we attempted to evaluate the feasibility of these mechanisms, both cellular mechanisms remain hypothetical. The hydrogen isotope systematics shown here contribute to put forward utility of δDCH4 value as a geochemical tracer of the origins of environmental CH4.