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Fumonisins are mycotoxins produced by Fusarium verticillioides, a filamentous fungus that is a widespread pathogen of corn. The biosynthesis of fumonisins is catalyzed by an iterative modular polyketide synthase (PKS). The study of the biosynthetic mechanism for these reduced fungal polyketides has been challenging due to the difficulties in detecting the intermediates with a linear carbon chain and manipulating the 7-domain PKS gene from the filamentous fungus. Here, we described the development of a genetic system for functionally manipulating the methyltransferase domain of FUM1 that is responsible for the assembly of a dimethylated 18-carbon chain. Using a two-stage screening strategy, including both positive and negative screenings, we were able to generate mutant strains with a specifically changed active-site in FUM1. LC-MS analyses indicated that biosynthetic intermediates were detectable in the early stage of culture. The results represent the first functional manipulation of the PKS involved in the biosynthesis of fumonisins.