The lipid biomarkers associated with various geothermal facies within Champagne Pool were investigated and compared with previous microbiological characterisation. Biomarker analysis revealed two distinct microbial communities spanning the margin of Champagne Pool: the first in the subaqueous domal stromatolites, subaqueous orange precipitate and spicular microstromatolites at the air-water interface, and the second in an acidic sinter from the overhanging ledge. Lipid biomarkers were detected in all facies and are consistent with previous microbiological analysis, suggesting that encapsulated biomarkers do record microbial community structure. Results suggest a microbial community principally comprising Aquificales, Thermodesulfobacteriales, Sulfolobus and Thermofilum populations in all facies. In the acidic sinter, additional bacterial (Actinomycetales and Planctomycetales), archaeal (Thermoplasmatales) and algal (Cyanidium caldarium) inputs were observed, the predominance of algal biomarkers suggesting that these organisms are major contributors to the microbial community in this facies. It is evident that local geochemistry plays a fundamental role in defining community composition and, consequently, microbial lipids entrained in Champagne Pool sinters, with metabolic activity of the microbial community reflecting the physicochemical conditions in each microenvironment.