Anomalously high concentrations of humic‐rich dissolved organic matter (DOM) in extant submarine hydrothermal vent plumes traveled far from source are increasingly being reported. This DOM, able to mobilize trace metals (e.g., Fe2+) has been hypothesized as originating from organic matter produced by thermogenic bacteria. To eliminate a possible abiogenic origin of this DOM, study is required of well‐preserved organic compounds that can be attributed to thermogenic bacteria. The Central Indian Ocean Basin (CIOB) is part of a diffuse plate boundary and an intraplate deformation zone. Coarse fraction (>63 µ) characteristics, mineralogy, magnetic susceptibility, and geochemistry were examined in sediments of a core raised close to a north‐south fracture zone near the Equator. Two horizons of distinctly brown‐colored sediments were shown as hydrothermally altered from their charred fragments and geochemistry (CaCO3, Corg, Ti/Al, Al/(Al + Fe + Mn), Sr/Ba, Mg/Li, Mn micronodules, Fe/Mn). We examined whether humic substances were preserved in these sediments, and if so whether their carbon isotope distribution would support their hydrothermal origin. Alkali extraction of sediments afforded humic acids (HA) in yields up to 1.2% in the brown sediments. The remaining portions of the core had nil or low concentrations of HA. The carbon of hydrothermal HA is isotopically heavier (average δ13C, ∼ −16.3‰) compared to nonhydrothermal HA (–18.1‰), suggesting that they were probably formed from organic matter that remained after elimination of lighter carbon enriched functional groups during diagenesis. The results provide compelling evidence of HA formation from lipids originating from thermogenic bacteria.