The increasing incidence of mass developments of Cyanobacteria in fresh- and brackish water is a matter of growing concern due to the production of toxins that threaten human and livestock health. The toxins that are produced by freshwater Cyanobacteria comprise hepatotoxins (cyclic peptides such as microcystins and nodularin, as well as alkaloids such as cylindrospermopsin) and neurotoxins (alkaloids such as anatoxin-a, anatoxin-a(S) and saxitoxins). The variation in toxicity between and within species of Cyanobacteria has been recognised for a long time. However, the toxic and non-toxic genotypes within a species cannot be discriminated under the microscope, which has been a major obstacle in identifying those factors that influence toxin production both in the laboratory and in the field. During the last decade, major advances were achieved due to the elucidation and functional characterisation of genes, such as the gene cluster encoding the synthesis of the hepatotoxic heptapeptide, microcystin. Genetic techniques, in particular, have been used to explore (i) the genetic basis, biosynthesis pathways, and physiological regulation of toxin (microcystin) production, (ii) gene loss processes resulting in a patchy distribution of the microcystin synthetase gene cluster among genera and species, as well as (iii) the distribution and abundance of the microcystin genes in the environment. In recent years, experience in detecting microcystin genes directly in the field has increased enormously and robust protocols for the extraction of DNA and the subsequent detection of genes by PCR (polymerase chain reaction)-based methods are now available. Due to the high sensitivity of PCR, it is possible to detect toxic genotypes long before a toxic cyanobacterial bloom may occur. Consequently, waterbodies that are at risk of toxic bloom formation can be identified early on in the growing season along with environmental factors that can potentially influence the abundance of toxin producing genotypes.