Late Pennsylvanian seep limestones (ca. 300 Ma) enclosed in the Ganigobis shales in southern Namibia formed by microbial activity. The process that induced carbonate precipitation was the anaerobic oxidation of methane. The presence of 13C-depleted pentamethylicosane (PMI) (−113‰) and a mixture of crocetane and phytane (−112‰) in concert with similarly 13C-depleted pseudohomologous series of regular isoprenoids reveals that methanotrophic archaea oxidized methane anaerobically at the ancient seep site. Biphytane and a C39 pseudohomologue are other archaeal molecular fossils with δ13C values of −99‰ and −97‰, respectively. The former presence of sulfate-reducing bacteria as the syntrophic partners of methanotrophic archaea in the anaerobic oxidation of methane is indicated by isotopically depleted iso- and anteiso-alkanes. These compounds most probably derive from non-isoprenoidal monoethers and diethers, synthates of sulfate-reducing bacteria. These findings show that anaerobic oxidation of methane is at least 300 m.y. old, extending the record of this process for ~140 m.y. As the molecular fossils of archaea and bacteria are preserved in a product of their own metabolic activity (i.e., methane-derived carbonates with δ13C values as low as −51‰), the syngenicity of molecular fossils and enclosing deposits is unambiguous. This reveals that microbially formed rocks can represent excellent archives for studying past biogeochemical processes.