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High abundances of 7- and 6-monomethylalkanes as well as C(17)n-alkane, indicative of cyanobacteria, have been discovered near the surfaces of Archean carbonate rocks of the Fortescue Group in the Pilbara region, Western Australia. The presence of cyanobacterial biomarkers is mostly limited to the surface layer (<1cm thickness) of the rocks, indicating that the cyanobacteria are an endolithic species. Biomarkers are found in bitumen I (solvent-extracted rock) and also in bitumen II (solvent-extracted decarbonated rock). The abundance of biomarkers is generally the same between both bitumen fractions in the surface layer, which suggests that the cyanobacteria penetrated into the carbonate minerals. Trace amounts of the biomarkers have also diffused into a deeper part of the rocks, but this influence is only seen in bitumen I. This implies that hydrocarbons moved toward the inside of the rock through pores and fissures in the rock fabric. In contrast, hydrocarbons in bitumen II, which mainly come from within the carbonate minerals, are isolated from the hydrocarbon migration from the outside of the rock and may be ancient indigenous organic matter. To the best of our knowledge, this is the first report of the past or modern inhabitation of cyanobacteria on Archean rocks in the Pilbara region for which hydrocarbon biomarker analyses was used.