In recent years, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) with cluster ion sources has opened new perspectives for the analysis of lipid biomarkers in geobiology and organic geochemistry. However, published ToF‐SIMS reference spectra of relevant compounds are still sparse, and the influence of the chemical environment (matrix) on the ionisation of molecules and their fragmentation is still not well explored. This study presents ToF‐SIMS spectra of eight glycerolipids as common target compounds in biomarker studies, namely ester‐ and ether‐bound phosphatidylethanolamine, ester‐ and ether‐bound phosphatidylcholine, ester‐bound phosphatidylglycerol, ester‐ and ether‐bound diglycerides and archaeol, obtained with a Bi cluster ion source. For all of these compounds, the spectra obtained in positive and negative analytical modes showed characteristic fragments that could clearly be assigned to e.g. molecular ions, functional groups and alkyl chains. By comparison with the reference spectra, it was possible to track some of these lipids in a pre‐characterised organic extract and in cryosections of microbial mats. The results highlight the potential of ToF‐SIMS for the laterally resolved analysis of organic biomarkers in environmental materials. The identification of the target compounds, however, may be hampered by matrix effects (e.g. adduct formation) and often require careful consideration of all spectral features and taking advantage of the molecular imaging capability of ToF‐SIMS. Copyright © 2009 John Wiley & Sons, Ltd.