We investigated the effect of CO2 and primary production on the carbon isotopic fractionation of alkenones and particulate organic matter (POC) during a natural phytoplankton bloom dominated by the coccolithophore Emiliania huxleyi. In nine semi-closed mesocosms (∼11 m3 each), three different CO2 partial pressures (pCO2) in triplicate represented glacial (∼180 ppmv CO2), present (∼380 ppmv CO2), and year 2100 (∼710 ppmv CO2) CO2 conditions. The largest shift in alkenone isotopic composition (4-5‰) occurred during the exponential growth phase, regardless of the CO2 concentration in the respective treatment. Despite the difference of ∼500 ppmv, the influence of pCO2 on isotopic fractionation was marginal (1-2‰). During the stationary phase, E. huxleyi continued to produce alkenones, accumulating cellular concentrations almost four times higher than those of exponentially dividing cells. Our isotope data indicate that, while alkenone production was maintained, the interaction of carbon source and cellular uptake dynamics by E. huxleyi reached a steady state. During stationary phase, we further observed a remarkable increase in the difference between δ13C of bulk organic matter and of alkenones spanning 7-12‰. We suggest that this phenomenon is caused mainly by a combination of extracellular release of 13C-enriched polysaccharides and subsequent particle aggregation induced by the production of transparent exopolymer particles (TEP). © 2007 Elsevier Inc. All rights reserved.