<jats:title>Abstract</jats:title><jats:p>The identification of a 36 kb welwitindolinone (<jats:italic>wel</jats:italic>) biosynthetic gene cluster in<jats:italic>Hapalosiphon welwitschii</jats:italic>UTEX B1830 is reported. Characterization of the enzymes responsible for assembling the early biosynthetic intermediates geranyl pyrophosphate and 3‐((<jats:italic>Z</jats:italic>)‐2′‐isocyanoethenyl)indole as well as a dedicated N‐methyltransferase in the maturation of<jats:italic>N</jats:italic>‐methylwelwitindolinone C isothiocyanate solidified the link between the<jats:italic>wel</jats:italic>pathway and welwitindolinone biosynthesis. Comparative analysis of the ambiguine and welwitindolinone biosynthetic pathways in two different organisms provided insights into the origins of diverse structures within hapalindole‐type molecules.