This study reports that a series of tryptophan derivatives with modifications on the side chain or at the indole ring were accepted by two cyclic dipeptide prenyltransferases, CdpNPT and FtmPT1, and converted to prenylated derivatives. The structures of the enzymatic products were elucidated by NMR and MS analyses. In comparison to cyclic dipeptides, which were reversely prenylated by CdpNPT at N-1 and in a regular manner by FtmPT1 at C-2, respectively, tryptophan and its simple derivatives were prenylated reversely by both enzymes at N-1. These results demonstrated the substrate promiscuity of both enzymes.