Upwelling coastal systems are of great interesting for Science, since they provide nutrientes and control the biology, the chemistry and fisheries in vast ocean areas. Cabo Frio ecosystem (RJ – located on the southwestern margin of the South Atlantic Ocean) is the main coastal upwelling zone in Brazil and it is an exception in global ocean, as major upwelling zones are located in ocean current systems of East margins. This seasonal upwelling is governed by winds pattern prevailing in the area and it causes intermittent but significant biological responses in the water column of Cabo Frio. Besides generating rather intense phytoplankton and zooplankton surges the enriched waters are responsible for proliferation of microorganisms in the sediments. As long as there are no relevant sources of land derived nutrients to the region, the coupling of physical and biological ocean processes control the transfer of organic material of planktonic origin to the sediments. In this work, lipid biomarkers analyzed in sediments sampled in two stations (CF02-01A and CF02-02A), located between 23 degree 11 S and 41 degree 47 W and collected in October/2002, were used to evaluate possible changes in the upwelling system during the late Holocene. Organic compounds were obtained through Soxhlet extraction technique, following saponification and the division in neutral and acid fractions. Neutral fraction was concentrated and then passed through a chromatographic column to separate n-alkanes from sterols and fatty alcohols and acids by CG-MS. In fatty acid fraction 31 compounds were identified and quantified while in neutral fraction 67 compounds were investigated. CF02-01A core was characterized by the average concentrations of 90,40 more or less 99,15 ug g-1 TOC for n-alkanes; 93,39 more or less 37,00 ug g-1 TOC for sterols; 81,32 more or less 40,65 ug g-1 TOC for fatty alcohols and 129,70 more or less 132,41 ug g-1 TOC for fatty acids. In CF-02A core the average concentrations obtained were: 128,7 more or less 213,11 ug g-1 TOC for n-alkanes; 68,25 more or less 30,02 ug g-1 TOC for sterols; 119,20 more or less 96,65 ug g-1 TOC for fatty alcohols and 100,13 more or less 176,88 ug g-1 TOC for fatty acids. These concentrations are smaller than the reported for upwelling systems in Africa and Peru. The results indicate that the organic matter in the Cabo Frio region is strongly influenced by highly labile autochthonous material derived from diatoms and dinoflagellates, although there is a significant influence of allochthonous organic matter possibly driven by eolic processes. An increase is observed in the accumulation rates of both autochthonous and allochthonous markers in the period between 3600 BP and 2100 BP, superimposed by oscillations with time intervals of about 300 years. Such trends are probably bound to variability of regional or semi-hemispheric circulation of the atmosphere, which are controlling the upwelling processes. It is important to highlight the presence of substantive UCM in many sample, which allied to the occurrence of maturated hopanes indicate presence of degraded oil residues. This is a strong evidence of oil seepage from reservoirs abundantly present in the region.