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Fossil pigments often preserve in lake sediments long after the morphological remains of most algae and bacteria are lost. In principle, analyses of sedimentary carotenoids, chlorophylls, their derivatives and other lipid-soluble pigments can be used to reconstruct historical changes in primary-producer community abundance and composition, so long as biomarkers are accurately isolated, identified and quantified. This chapter summarizes a series of practical techniques in order to familarize investigators with the potential and pitfalls inherent in fossil pigment analyses. First we describe the common uses of sedimentary pigments in paleolimnology and summarize knowledge of pigment biogeochemistry and taphonomy, especially as concerns water-column processes. Second we review a series of practical procedures to collect, isolate and quantify pigments, particularly by high performance liquid …