The aim of this study was to analyze and compare the relationship between environmental factors (temperature; pH; total phosphorus - TP and nitrogen - TN and their ratio) and occurrence of microcystin producing cyanobacteria in two shallow, eutrophic Polish water bodies, Sulejów Reservoir (Central Poland) and Bnińskie Lake (Western Poland). Samples for analyses were collected from June till October 2005. Cyanobacteria Microcystis aeruginosa and Planktothrix agardhii, responsible for microcystins production, were detected respectively for Sulejów Reservoir and Bnińskie Lake. Molecular analysis of the mcyE gene, indicated the presence of toxigenic strains of cyanobacteria in both water bodies throughout the whole sampling period. The highest extracellular microcystins toxicity established by PPIA was 2.83 μg dm-3 and 2.19 μg dm-3 in samples dominated by M. aeruginosa and P. agardhii respectively. Two different environmental factors in studied water bodies were crucial in occurrence of hepatotoxic cyanobacteria. The strong correlation between biomass of M. aeruginosa and total nitrogen (TN) in Sulejów Reservoir (R=0.83; p<0.05) was observed. Strong negative correlation was found between biomass of P. agardhii and temperature (R=-0.77; p<0.05 and R=-0.70; p<0.05) in Bnińskie Lake.
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