<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS secondary metabolic pathway. They are produced by a variety of cyanobacteria and are responsible for the poisoning of humans as well as the deaths of wild and domestic animals around the world. The chemical diversity of the microcystin family is attributed to a number of genetic events that have resulted in the diversification of the pathway for microcystin assembly. </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Here, we show that independent evolutionary events affecting the substrate specificity of the microcystin biosynthetic pathway have resulted in convergence on a rare [<jats:italic>D</jats:italic>-Leu<jats:sup>1</jats:sup>] microcystin-LR chemical variant. We detected this rare microcystin variant from strains of the distantly related genera <jats:italic>Microcystis</jats:italic>, <jats:italic>Nostoc</jats:italic>, and <jats:italic>Phormidium</jats:italic>. Phylogenetic analysis performed using sequences of the catalytic domains within the <jats:italic>mcy</jats:italic> gene cluster demonstrated a clear recombination pattern in the adenylation domain phylogenetic tree. We found evidence for conversion of the gene encoding the McyA<jats:sub>2</jats:sub> adenylation domain in strains of the genera <jats:italic>Nostoc</jats:italic> and <jats:italic>Phormidium</jats:italic>. However, point mutations affecting the substrate-binding sequence motifs of the McyA<jats:sub>2</jats:sub> adenylation domain were associated with the change in substrate specificity in two strains of <jats:italic>Microcystis</jats:italic>. In addition to the main [<jats:italic>D</jats:italic>-Leu<jats:sup>1</jats:sup>] microcystin-LR variant, these two strains produced a new microcystin that was identified as [Met<jats:sup>1</jats:sup>] microcystin-LR. </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Phylogenetic analysis demonstrated that both point mutations and gene conversion result in functional <jats:italic>mcy</jats:italic> gene clusters that produce the same rare [<jats:italic>D</jats:italic>-Leu<jats:sup>1</jats:sup>] variant of microcystin in strains of the genera <jats:italic>Microcystis</jats:italic>, <jats:italic>Nostoc</jats:italic>, and <jats:italic>Phormidium</jats:italic>. Engineering pathways to produce recombinant non-ribosomal peptides could provide new natural products or increase the activity of known compounds. Our results suggest that the replacement of entire adenylation domains could be a more successful strategy to obtain higher specificity in the modification of the non-ribosomal peptides than point mutations. </jats:sec>