Lipids represent an integral part of cellular membranes and are important sources of energy storage for many organisms. Among the variety of structures synthesized across bacteria to fish, some provide important taxonomic markers of their origin and reflect metabolic processes. Using detailed structural analysis, we have used lipid as biomarkers to trace the variety of organisms’ present in marine waters, the interactions across trophic levels and the role of bacteria in carbon turnover. Together with isotopic analysis and other measures, this presentation will provide some examples of our work in polar waters to use lipids to help trace the cycling of organic carbon from its initial synthesis to its long-term preservation in sediments.”