Treatment of methyl indole-3-carboxylate with bromine in acetic acid gives methyl 5,6-dibromoindole-3-carboxylate regioselectively, from which the parent 5,6-dibromoindole can be accessed via a one-pot, microwave-mediated ester hydrolysis and decarboxylation. Application of these building blocks in syntheses of natural and non-natural 5,6-dibromoindole derivatives, including meridianin F and 5,6-dibromo-2′-demethylaplysinopsin, is reported.