Abstract: UbiA membrane-bound aromatic prenyltransferases (UbiA PTs) catalyze the transfer of prenyl moieties to aromatic acceptor molecules to form C-C or C-O bonds, and participate in the biosynthesis of important plant chemicals, including ubiquinone, plastoquinone, chlorophyll, and tocopherol. A variety of aromatic secondary metabolites with prenyl groups in plants are also products of this class of enzyme. The introduction of prenyl groups increases the structural diversity and biological activity of natural products. In this paper, we introduce the basic types of UbiA families in plants, summarize the substrate selectivity and catalytic characteristics of 57 UbiA PTs related to biosynthesis of secondary metabolites (flavonoids, coumarins, stilbenes), and discuss their phylogenetic relationship with primary metabolism-related PTs. We also discuss the exploration strategies of prenyltransferase genes and the application prospects of targeted synthesis of active prenylated compounds by microbial metabolic engineering.