<jats:title>Summary</jats:title><jats:p>Coronafacoyl phytotoxins are secondary metabolites that are produced by various phytopathogenic bacteria, including several pathovars of the Gram‐negative bacterium <jats:italic>Pseudomonas syringae</jats:italic> as well as the Gram‐positive potato scab pathogen <jats:italic>Streptomyces scabies</jats:italic>. The phytotoxins are composed of the polyketide coronafacic acid (CFA) linked via an amide bond to amino acids or amino acid derivatives, and their biosynthesis involves the <jats:italic>cfa</jats:italic> and <jats:italic>cfa‐</jats:italic>like gene clusters that are found in <jats:italic>P. syringae</jats:italic> and <jats:italic>S. scabies</jats:italic>, respectively. The <jats:italic>S. scabies cfa‐</jats:italic>like gene cluster was previously reported to contain several genes that are absent from the <jats:italic>P. syringae cfa</jats:italic> gene cluster, including one (<jats:italic>oxr</jats:italic>) encoding a putative F<jats:sub>420</jats:sub>—dependent oxidoreductase, and another (<jats:italic>sdr</jats:italic>) encoding a predicted short‐chain dehydrogenase/reductase. Using gene deletion analysis, we demonstrated that both <jats:italic>oxr</jats:italic> and <jats:italic>sdr</jats:italic> are required for normal production of the <jats:italic>S. scabies</jats:italic> coronafacoyl phytotoxins, and structural analysis of metabolites that accumulated in the Δ<jats:italic>sdr</jats:italic> mutant cultures revealed that Sdr is directly involved in the biosynthesis of the CFA moiety. Our results suggest that <jats:italic>S. scabies</jats:italic> and <jats:italic>P. syringae</jats:italic> use distinct biosynthetic pathways for producing coronafacoyl phytotoxins, which are important mediators of host‐pathogen interactions in various plant pathosystems.