Despite lack of efficient physical protection in the highly competitive and hostile environment, the marine invertebrates including soft corals and gorgonians can survive mainly relying on their chemical defensive system by a series of secondary metabolites accumulating in their bodies or releasing to their surroundings. The chemical defensive functions of these secondary metabolites were found to serve as antifeedant, antimicrobial, antifouling agents as well as allelopathicsubstances. Chemical study on the defensive substances from corals and gorgonians is one of the most important topics in marine chemical ecology. The research results could help us to understand the chemical ecology relationships between corals and their surrounding organisms. The research strategy and methodology played an edificatory role in the bioactive natural products discovery and new drug lead compound generation from marine sources. The research progress on chemical defensive substances from soft corals and gorgonians was reviewed. This review focused on the structures of these secondary metabolites as well as their functions including antipredatory, allelopathic, and antifouling activities.