The present study deals with the molecular genetics and biochemistry of two cyanobacterial toxins, cylindrospermopsin and saxitoxin. The molecular phylogenies of three putative cylindrospermopsin biosynthesis genes, encoding an amidinotransferase (aoaA), a non-ribosomal peptide synthetase (aoaB) and a polyketide synthase (aoaC) has been examined and functional modelling was carried out to gain insights into the mechanism of precursor recruitment in this pathway. An in vitro assay was developed to characterise biochemical requirements for saxitoxin biosynthesis, using enzyme extracts from Cylindrospermopsis raciborskii T3. All biosynthesis enzymes were located in the cytosol. The effects of substrates and inhibitors on the in vitro biosynthesis of saxitoxin were examined and predictions made regarding enzymes that may be involved. These predictions were used in a degenerate PCR approach to identify the saxitoxin biosynthesis gene cluster in cyanobacteria.