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Cladoniamides are a set of bisindole compounds that contain an indolotryptoline rather than the more common indolocarbazole scaffold. Besides their interesting structures, several of the cladoniamides have been found to be potent cytotoxic agents. We set out to isolate the brominated analogues of known cladoniamides by supplementing the fermentation medium with KBr, which led to the production of 5-bromocladoniamide A. However, the observed production levels were very low. To determine whether the selection against the bromo-substrates is early or late in the cladoniamide biosynthetic pathway, we synthesized 3-chloroarcyriaflavin and 3-bromoarcyriaflavin. These substrates were then fed into Streptomyces albus + cla (ΔclaC), which contains the complete cladoniamide biosynthetic pathway, except one crucial gene required for the production of cladoniamides. Through the feeding experiment, we found approximately equal amount of incorporation of the chloro and bromo substrates. The results suggest that the substrate selectivity against bromo precursors is upstream in the pathway from the enzyme encoded by the inactivated gene. Overall, we have observed the production of brominated cladoniamides through the two different methods of modifying the growth conditions and of precursor directed biosynthesis. Furthermore, this work presents a facile way to generate new indolotryptoline molecules through synthetic generation of desired indolocarbazole substrates and then biological conversion using the cladoniamide biosynthetic pathway.