Abstract In our continuous concern of biodiversity relating to molecular structures in Sabang island, we found complex species of soft coral (genus Lobophytum ). Molecular phylogenetic analysis on 82 specimens confirmed the presence of Lobophytum crassum , Lobophytum verum , and Lobophytum rigidum . On the other hand, the identification of chemical profiles was performed by spectroscopy analysis based on metabolomics approaches. As a result, we identified the chemical diversity of cembrane-type diterpenoids class from all specimens. Moreover, metabolomics analysis using feature-based molecular networking showed L. crassum , L. verum , and L. rigidum genes poses fundamental roles in the formation of chemical variations. Our results indicated that cembrane-type diterpenoids were found on all species related to genus Lobophytum in Sabang island, located in the western part of the Indonesian archipelago.