In this study, we investigated the potential antilarval and antibacterial activity of secondary metabolites of the gorgonians Subergorgia suberosa and Scripearia gracillis from the South China Sea. Fresh specimens of these two gorgonian corals were collected from a shallow reef in Sanya Bay of Hainan Island and extracted with different solvents. Antilarval activity of the chemical extracts and pure compounds was evaluated in settlement inhibition assays with laboratory-reared Balanus amphitrite and Bugula neritina larvae, while antibacterial activity was assessed with disc diffusion bioassay on growth inhibition of 15 marine bacterial species. Using bioassay-guided procedures, we purified and identified nine compounds. The most potent metabolites produced by these gorgonian corals were subergorgic acid and pregn-4-ene-3, 20-dione extracted from S. suberosa. Our results show that the gorgonian coral S. suberosa and S. gracillis can produce potent anti-fouling compounds that deserve further exploration.