AbstractThe aim of this study was early genetic identification of microcystin‐producing cyanobacteria and monitoring their toxigenicity by determining toxin concentrations in three Polish lakes throughout the summer of 2004. The assessment of cyanobacterial blooms was carried out in shallow, eutrophic water bodies: Lake Jeziorak, Lake Bninskie, and Sulejow Reservoir. Samples for DNA, phycological, and toxin analyses were collected from July till October. Molecular analysis of the 16S rRNA region was used to detect cyanobacteria in water samples. The microscopic analysis was performed to investigate seasonal variation of phytoplankton. Cyanobacteria, with domination by Microcystis, Planktothrix, and Planktolyngbya were detected during the whole monitoring period in Sulejow Reservoir, Lake Bninskie, and Lake Jeziorak, respectively. The presence and identification of toxic strains in water bodies was studied by PCR amplification of mcy genes in the microcystis synthesis pathway. The presence of the mcyA, mcyB, mcyD, and mcyE genes in water samples indicated the genetic potential to produce microcystins. Toxicity of water samples and microcystin concentrations were established by PPIA and HPLC, respectively. The maximum concentration of microcystins was 11.13 μg/L and 4.67 μg/L in samples dominated by P. agardhii and M. aeruginosa, respectively. Molecular analysis showed that toxigenic strains of cyanobacteria occurred in the three lakes throughout the summer season. © 2006 Wiley Periodicals, Inc. Environ Toxicol 21: 380–387, 2006.