Eleven waterbodies in Western France dominated by cyanobacteria of the genera Aphanizomenon and Anabaena were analyzed in September 2006 for microcystins (MC) and cylindrospermopsin (CYN). CYN was detected for the first time in France in four of them in the presence of Aphanizomenon flos-aquae and in the presence of Anabaena planctonica in the other. The intracellular concentrations of CYN measured by LC-MS/MS ranged between 1.55 and 1.95 μg/L. The occurrence of CYN represents an additional health hazard to MC especially because Aphanizomenon flos-aquae is the third most common species in freshwaters in France. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.