Stable carbon isotopes (12C and 13C) are widely used to trace biogeochemical processes in the global carbon cycle. Natural fractionation of carbon isotopes is mainly due to the discrimination of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) against 13C during photosynthesis. In marine and other aquatic microorganisms, this fractionation is lowered when the dissolved CO2 (CO2(aq)) is decreasing, but the underlying mechanisms are poorly understood. Cultured Synechococcus PCC7942 showed maximum isotopic fractionations of -33omicron (in delta 13C units) relative to the total inorganic carbon (Ci) when CO2(aq) is above 30 m M. As the culture grew, pH increased, CO2(aq) was lower than 1 m M, and the Ci concentrating mechanism was induced although the Ci was above 3 mM. The isotopic fractionation was drastically reduced to values of -1 to -3 omicron relative to Ci. A simple carbon isotope flux model suggests that during the first stages of the experiment the total uptake (F1) was roughly three- to four-fold greater than the photosynthetic net accumulation (F2). When the Ci concentrating mechanism was induced, the leakage of CO2 from the cells declined, the cells started to utilize HCO3- and the F1/F2 ratio decreased to values close to 1. Based on this model the isotopic variability of oceanic phytoplankton suggests that the F1/F2 ratio may be above 3 in high latitudes and ~1.1 in equatorial waters, where the Ci concentrating mechanism is probably induced. Attempts to reconstruct past atmospheric CO2 levels and paleoproductivity should take into account the effects of the Ci concentrating mechanism on the isotopic fractionation of aquatic primary producers.Key words: carbon concentrating mechanism, carbon isotope fractionation, CO2, photosynthesis.