Cylindrospermopsin (CYN) is a potent hepatotoxin produced by different cyanobacteria of the order Nostocales, which is widely distributed in freshwaters and considered a hazard to wildlife and humans. In Europe, only Aphanizomenon flos-aquae is identified as CYN producer so far and the seasonal variability of CYN was not studied yet. Therefore, we studied the seasonal dynamics of the particulate and dissolved CYN concentrations in relation to the cyanobacterial occurrence and environmental factors in two German lakes over two years. Total CYN reached maximum concentrations of 0.34 and 1.80 µg L-1 in Melangsee and Langer See, respectively. In both lakes, the dissolved CYN fraction peaked after the particulate fraction, and reached higher values indicating that CYN is poorly decomposed and accumulates in the water. The cyanobacterial community was very diverse in both lakes, including potentially CYN producing species such as Cylindrospermopsis raciborskii, Anabaena bergii and Aphanizomenon flos-aquae. However, these species could be excluded as the major CYN producers. The stronges significant correlation was found for Aphanizomenon gracile and CYN, strongly indicating that the species is the main CYN producer in Langer See. CYN was also correlated with Planktothrix agardhii in Langer See and Pseudanabaena limnetica in Melangsee, but species of the order scillatoriales are not known to produce CYN. In Melangsee the CYN producer could not be identified. Different correlations of CYN with abiotic factors in the two lakes indicate the presences of further undetected CYN producers as well as different regulation mechanisms of their dynamic and the variability of CYN.