An astonishing variety of different lipids have been found in marine sediments and the water column attesting to the diversity of biosynthetic pathways employed by aquatic organisms. Many of these compounds have distinctive structures allowing them to be used as biomarkers for particular sources of organic matter in marine ecosystems. Microalgae synthesize many unusual compounds, such as long-chain alkenones, alkenoates and alkenes, long-chain alkyl diols, highly branched isoprenoid alkenes as well as distinctive sterols and unsaturated fatty acids, thus enabling inputs of microalgal organic matter to be easily recognized. The input of terrestrial organic matter to marine environments can be recognised from lipids of higher plant origin, such as long-chain alcohols, alkanes and fatty acids, and C 29 sterols, although marine sources for some of these compounds are now recognised. Bacteria synthesize a diverse range of compounds, such as branched fatty acids, hopanoids and isoprenoids, many of which are particularly stable, for instance those that contain an ether bond. Qualitative assignments of organic matter sources are thus reasonably straightforward, although even now lipids can be found for which no source is known. However, quantitative assessments are more difficult since lipid contents vary greatly between different organisms and lipids display a wide range of reactivities. The combination of lipid biomarker data with information from stable isotopes can provide good estimates of organic matter sources, provided that the isotope signatures of the contributing sources (end-members) are known. This chapter provides a review of biomarkers commonly found in sediments together with notes on their identification and source specificity.