Prenyltransferases catalyze prenyl groups to a wide variety of acceptors, such as isoprenoid groups, aromatic compounds, and proteins. Those that catalyze the attachment of a prenyl moiety to an aromatic nucleus are known as “aromatic prenyltransferases”. Prenylated aromatic compounds constitute a massive number of biologically active molecules such as ubiquinones, plastoquinones, vitamin E, prenylflavonoids and fungi metabolites. This paper presents advances in molecular studies of aromatic prenyltransferases in plants and fungi, focusing on membrane-bound homogentisate prenyltransferases involved in the biosynthesis of plastoquinones and vitamin E, flavonoid prenyltransferases, and soluble indole prenyltransferases.