GuA6DT, a flavonoid prenyltransferase, was identified from Glycyrrhiza uralensis, and it was found that this enzyme regiospecifically transfers a dimethylallyl moiety to apigenin at the C-6 position. A further substrate specificity investigation indicated that the existence of hydroxyls at both the C-5 and C-7 positions of the flavone skeleton is critical for the prenylation. However, substitutions on the B-ring had negligible influence on the prenylation. A comparison of GuA6DT expression in different organs revealed that mRNA is mainly expressed in the aerial parts. Moreover, the GuA6DT mRNA was found to be regulated at the transcriptional level, because methyl jasmonate induced upregulation in cultured cells. GuA6DT is the first identified flavone prenyltransferase to exhibit strict substrate specificity and regiospecificity.