Previous biomarker studies of microbes involved in anaerobic oxidation of methane (AOM) have targeted non-polar lipids. We have extended the biomarker approach to include intact polar lipids (IPLs) and show here that the major community types involved in AOM at marine methane seeps can be clearly distinguished by these compounds. The lipid profile of methanotrophic communities with dominant ANME-1 archaea mainly comprises diglycosidic GDGT derivatives. IPL distributions of microbial communities dominated by ANME-2 or ANME-3 are consistent with their phylogenetic affiliation with the euryarchaeal order Methanosarcinales, i.e., the lipids are dominated by phosphate-based polar derivatives of archaeol and hydroxyarchaeol. IPLs of associated bacteria strongly differed among the three community types analyzed here; these differences testify to the diversity of bacteria in AOM environments. Generally, the bacterial members of methanotrophic communities are dominated by phosphatidylethanolamine and phosphatidyl-(N,N)-dimethylethanolamine species; polar dialkylglycerolethers are dominant in the ANME-1 community while in ANME-2 and ANME-3 communities mixed acyl/ether glycerol derivatives are most abundant. The relative concentration of bacterial lipids associated with ANME-1 dominated communities appears significantly lower than in ANME-2 and ANME-3 dominated communities. Our results demonstrate that IPL analysis provides valuable molecular fingerprints of biomass composition in natural microbial communities and enables taxonomic differentiation at the rank of families to orders. © 2008 Elsevier Ltd. All rights reserved.