‘Blooms’, an increasing worldwide phenomenon, are adversely affecting surface water resource, including reservoirs and lakes, used for drinking water supplies, recreation, crop, irrigation and fisheries. These amenities are affected by recurrent mass proliferations of cyanobacteria. The latter are responsible for the production of a wide range of bioactive compounds, including potent toxins (cyanotoxins). These comprise neurotoxins, cytotoxins, inflammatory agents, and hepatotoxins. Microcystins (MCs), hepatotoxins and tumour promoters are the most documented of the cyanotoxins. The microcystin synthetase gene cluster (mcy) involved in MC biosynthesis consists of a succession of non-ribosomal peptide synthase (NRPS) and polyketide synthetase (PKS) genes. The main producers of MCs are Anabaena, Microcystis, and Planktothrix. However, it is not possible to distinguish a toxic from a non-toxic strain on the basis of their morphology. In the present study, molecular tools were used, optimized and developed to (i) characterize the 16S rRNA gene diversity of planktonic cyanobacteria, (ii) to detect the cyanobacteria responsible for the production of MCs, (iii) to identify the MCs producing taxa, and (iv) to determine the environmental factors that influence the dynamic of toxic and non-toxic genotypes in Belgian freshwaters. Eighty-nine strains were isolated and their 16S rRNA genes sequenced. The 16S rRNA gene diversity was studied in 32 samples by denaturing gradient gel electrophoresis (DGGE). In order to evaluate the contribution of this work to the study of the molecular diversity of cyanobacteria in Belgian waterbodies, 114 (strains and DGGE) sequences obtained during this PhD thesis were compared to Belgian sequences obtained by others. As a result, 14 previously undiscribed operational taxonomic units (OTUs) were found in the present study. For polymerase chain reaction (PCR) detection of the mcyA/B/E genes, the DNA from a total of 162 environmental samples was extracted. The three genes were found together in ...