The structure of the major peptide produced by Microcystis cf. wesenbergii NIVA-CYA 172/5, the halogenated heptapeptide cyanopeptolin-984, was determined using LC/MS/MS. A gene cluster encoding a peptide synthetase putatively producing a cyanopeptolin was cloned from the same strain and sequenced. The cluster consists of four genes encoding peptide synthetases and one gene encoding a halogenase. Two additional ORFs transcribed in the opposite direction were found in the 5' flanking sequence; one of these encodes an ABC transporter. The overall organization of the cyanopeptolin synthetase operon (mcn) resembles a previously analysed anabaenopeptilide synthetase operon (apd) from Anabaena strain 90. Phylogenetic analyses of the individual domains from Mcn, Apd and other cyanobacterial peptide synthetases showed clustering of the adenylation domains according to function irrespective of operon origin - indicating strong functional constraints across peptide synthetases. In contrast, the condensation and thiolation domains to a large extent grouped according to operon affiliation or position in the respective operons. Phylogenetic analyses of condensation domains indicated that N-terminal domains and domains that condense L-amino acids and D-amino acids, respectively, form three separate groups. Although recombination events are likely to be involved in the evolution of mcn, no clear evidence of genetic recombination between the two cyanopeptolin gene clusters was found. Within the genus Microcystis, microcystin and cyanopeptolin synthetases have an evolutionary history of genomic coexistence. However, the data indicated that the two classes of peptide synthetase gene clusters have evolved independently.