Freshwater cyanobacteria produce a wealth of biologically active metabolites, which can adversely affect human and animal health, and cause great economic damage to the fishing, tourism and water-management industries on a global scale. We describe the molecular genetics and biochemistry of biosynthesis for the cyanobacterial toxic alkaloids cylindrospennopsin, paralytic shellfish toxins (PST) and anatoxin-a. Characterisation of the 43 kb cylindrospennopsin biosynthesis gene cluster (cyr), in Cylindrospermopsis raciborskii AWT205 is described. Biosynthesis is initiated via an amidinotransfer onto glycine followed by five polyketide extensions. Rings are formed via Michael additions, while the uracil ring is formed by a novel mechanism. Tailoring reactions, including sulfation and hydroxylation complete the biosynthesis. We describe the characterisation of PST biosynthesis gene clusters in Anabaena circinalis, Aphanizomenon sp. and Lyngbya wollei. These gene clusters span between 28 and 36 kb and contain genes coding for the biosynthesis and export of PSTs. The Lyngbya wollei PST gene cluster represents a 'natural combinatorial biosynthesis' event, explaining its unique toxin profile. A biosynthetic pathway leading to the formation of saxitoxin and its analogues in these organisms is proposed, and a putative insertion/excision site of the PST gene cluster in Anabaena circinalis 310F was identified. Interestingly, PSTs are produced by distantly related organisms via this unique biosynthesis pathway. We Investigated the phylogenetics of PST biosynthesis genes from four different genera of cyanobacteria. The results suggested that PST biosynthesis in cyanobacteria is an ancient trait, whereby the sporadic distribution of PST production in extant isolates of Anabaena circinalis and Aphanizomenon sp. is a result of the repeated loss of the biosynthetic gene cluster. Horizontal gene transfer also appears to have had a critical influence on PST biosynthesis in Lyngbya wollei. We additionally propose a hypothetical, mixed non-ribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) biosynthesis scheme for anatoxin-a. Degenerate PCR primers were developed, for the specific amplification of mixed NRPSIPKS hybrid ketosynthase (KS) domains. Gene-walking distally to a novel hybrid KS domain in the anatoxin-a producer Planktothrix rubescens, revealed an orphan gene cluster, denoted pro, which spans 24 kb and codes for a mixed NRPS/PKS system, putatively producing an acetylated and sulphated dipeptide.