The increasing demand for new lead compounds in the pharmaceutical and agrochemical industries has driven scientists to search for new sources of bioactive natural products. Marine invertebrates are a rich source of novel, bioactive secondary metabolites and they have attracted a great deal of attention from scientists in the fields of chemistry, pharmacology, ecology, and molecular biology. During the past 25 years, many complex and structurally unique secondary metabolites have been isolated from the invertebrates inhabiting the South China Sea. These metabolites are responsible for various bioactivities such as anti-tumor, anti-inflammation and antioxidant activities, and/or they act on the cardiovascular system. This review will focus on the marine natural product chemistry of invertebrates from the South China Sea, aiming to give the reader a brief view of the compounds isolated from these invertebrates, as well as their biological activities. The article covers the literature published during the period from the beginning of 1980 to the end of 2005, with 340 citations and 811 compounds from invertebrates from the South China Sea, including sponges, coelenterates, molluscs and echinoderms.