Lipid biomarkers and the organic carbon content have been determined in sediments collected from two transects across the continental shelf and slope (100 to 1500 m) in the oligotrophic Cretan Sea (Eastern Mediterranean). In general, concentrations (absolute and with respect to total organic carbon) of most biomarkers of both marine and terrestrial origin are attenuated with depth and with increasing distance from land. The low abundance of compounds that can be ascribed to primary producers (PP) (247–3589 ng/g of sediment and 5.2 to 23.6% of total lipids), namely diatoms, coccolithophorids, dinoflagellates, and nanoplankton species, reflects the low productivity in surface waters, along with the significant re-working of planktonic organic material prior and/or after burial. This re-working has been attributed to microorganisms, zooplankton and benthic invertebrates, with their specific biomarkers concentrations ranging from 111 to 755 ng/g (microorganisms) and from 157 to 2963 ng/g (zooplankton and invertebrates). Finally, the results on the abundance of terrestrial n-alkanals, n-alkanols and n-alkanoic acids, conjointly with those on terrestrial n-alkanes, presented in a previous paper (Mar. Chem. 68 (2000) 265) show that the terrestrial signal is an important fraction of total lipids in Cretan Sea sediments (13.0% to 51.7%). Its relative abundance shows an increase from the shallow station of the continental shelf (23.2%) to the deep basin station (51.7%), indicating a more persistent character of the terrestrially derived compared to the marine-derived component.