The prenylation of aromatic compounds plays an important role in the natural product research because it not only gives rise to an astounding diversity of primary and secondary metabolites in plants, fungi and bacteria but also enhances the bioactivities and bioavailabilities of these compounds. However, further investigation of prenylated aromatic compounds is frequently hindered due to their low content in nature and difficulties in chemical synthesis. Cloning aromatic prenyltransferase genes followed by heterologous expression would be attractive tools for the chemoenzymatic synthesis of bioactive molecules. This review summarizes the classifications, structural investigations, enzymatic catalysis and other progress in aromatic prenyltransferases originated from microorganisms.