The formation of isoprenylated phenolic compounds is catalyzed by prenyltransferase from the UbiA family, which transfer isoprenyl groups to the backbone of aromatic compounds. The isoprenylation of aromatic compounds increases the lipophilic properties and affinity to biomembranes, resulting in the formation of various bioactive molecules that play important roles in plant defense and human health. In this article, a total of 540 isoprenylated phenolic compounds, including 380 flavonoids, 80 coumarins, 27 quinones, 32 stilbenes, 16 p-hydroxybenzoic acids and 5 phenylpropionic acids were systematically reviewed in terms of their substituent groups, substituent positions and distribution in plants. So far, there are more than 30 of aromatic prenyltransferase identified in plants, and the substitution sites are relatively single. This review provided valuable reference in the selection of acceptor and donor molecules, thus aiding the identification of more prenyltransferase.