Secondary metabolites are bioactive compounds that demonstrate a broad chemical diversity and represent a source of pharmacologically and industrially relevant compounds. Bioactivities of secondary metabolites can be improved through chemical modification, or in vivo using an organism as a cell factory. As such, secondary metabolite modifications were examined in vivo using the Aspergillus niger secondary metabolite TAN-1612/BMS-192548 (TAN/BMS). The genes involved in the biosynthesis of TAN/BMS are organized in a biosynthetic gene cluster, and consist of a polyketide synthase backbone, tailoring enzymes including an O-methyltransferase, a transporter, and a fungal-specific transcription factor. In general, methyl group addition represents a strategy used to modify and optimize drugs, and methyltransferases represent an opportunity to explore methylation in vivo. Selective methylation was examined in a TAN/BMS overexpression and knockout strain through the homologous insertion of genes. To this end, an intraspecies methyltransferase gene library was designed and overexpressed in A. niger at the glucoamylase A (glaA) locus which is often exploited for enzyme overproduction. Screening methods were used to examine the expression profiles of the gene-edited strains. The overexpression of the native TAN/BMS methyltransferase gene in glaA was shown to partially restore TAN/BMS methylation. The methyltransferase mutants did not recapitulate nor modify the methylation pattern of TAN/BMS. Results indicated that the localization of genes may play an important role in selective methylation.