Gene duplication provides the key materials for new genes and novel functions. However, the mechanism underlying functional innovation remains unknown. In this study, we revealed the evolutionary pattern of the prenyltransferases of the UbiA gene family in 15 higher plants. Prenyltransferases of the UbiA gene family are involved in many important biological processes of both primary and secondary metabolism. Based on the phylogenetic relationships of the UbiA genes, seven subfamilies are classified. Confirming this classification, genes within each subfamily are characterized by similar exon numbers, exon lengths and patterns of motif combinations. Similar numbers of UbiA genes are found in different species within each subfamily except for Subfamily I, in which a Phaseoleae-specific expansion is detected in clade I-A. Homologous genes in clade I-A evolve rapidly, exchange sequences frequently and experience positive selection. Genes in clade I-A function as flavonoid prenyltransferase synthesis secondary compounds, while other genes from Subfamily I encode homogentisate phytyltransferase, which plays a role in primary metabolism. Thus, our results suggest that the secondary metabolism genes acquire new functions from those of primary metabolism through gene duplication and neofunctionalization driven by positive selection.