Although TSs derived from corals have been identified, a thorough understanding of their catalytic mechanisms-essential for shedding light on the natural evolution of these enzymes in corals-and the diversity of TSs among various coral species continues to be elusive. In our research, we performed a genome mining-based analysis on the sea whip coral, Paramuricea clavata, which resulted in the identification of a wide array of isoprenoid-related genes. This includes the discovery of 9 polyprenyl synthase genes and 11 TS genes. By evaluating the sequence similarity and conducting functional assessments of these 11 TS genes, we successfully identified a biflorane synthase (labeled as PcTS1), a germacrene B synthase (labeled as PcTS2), and multiple farnesol synthases. Through the use of isotope labeling studies, mutations informed by crystal structures of enzymes, QM/MM calculations, and phylogenetic analysis of TSs involved in the biosynthesis of biflorane, eunicellane, and cembrane, we obtained crucial insights into the evolution relationship between terpene scaffolds and TS genes among coral populations.