An Oligocene cold‐seep limestone (Lincoln Creek Formation, Washington State, USA) was studied for its lipid biomarker inventory. Biomarker analysis on minute amounts of sample (tens of mg) and complementary 13Ccarbonate analyses allowed us to link biogeochemical processes with individual, closely intertwined carbonate phases. The ancient seep deposit exhibits four major carbonate phases, according to the paragenetic sequence of (I) micrite, (II) yellow aragonite, (III) clear aragonite and (IV) equant calcite spar. For the micrite, varying but significant amounts of archaea‐derived isoprenoids clearly indicate that the precipitation of this phase was induced by the microbial anaerobic oxidation of methane (AOM). However, water column‐derived lipids present in this carbonate phase reflect the incorporation of organic matter from background sediment cemented by authigenic micrite. Yellow aragonite made up only a minor rock component (<10% vol.), but contained a major portion of lipid biomarkers indicative of AOM. Along with low δ13Ccarbonate values (less than −30‰ Pee Dee Belemnite), this points to an intimate spatial association of AOM consortia with the precipitation of yellow aragonite. Clear aragonite showed similar δ13Ccarbonate values but much lower, if any, contents of AOM biomarkers. This suggests that AOM‐derived carbonate ions diffused over a greater distance to the site of precipitation compared with yellow aragonite. The latest phase, equant calcite spar, did not yield appreciable biomarkers, but showed a notable 13Ccarbonate‐enrichment that is most likely caused by methanogenesis that prevailed in the sediments after AOM activity had ceased. A comparison of the ancient seep carbonates with modern counterparts from Hydrate Ridge (offshore Oregon, USA) revealed a remarkable coincidence of the respective mineral phases and their biomarker patterns. This suggests that the mechanisms of carbonate formation and the associated biogeochemical processes remained unchanged over geological times. □Biomarkers, carbonates, cold seeps, Hydrate Ridge, isotopes, Oligocene, Washington.

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