The South China Sea (SCS) is one of the world’s richest marine biodiversity areas, with abundant and diverse marine resources. In recent years, however, due to rapid economic development and population growth, marine biodiversity in the SCS is being lost. Beginning in 1991, the participants in the Informal Workshop on Managing Potential Conflicts in the South China Sea (the SCS Workshop) agreed to recommend to the relevant governments to explore areas of cooperation in the SCS, which include the study of marine biodiversity. As a result, in March 2002, a joint biodiversity project was carried out around the undisputed Indonesian Islands of Anambas in the SCS. Other joint biodiversity projects have also been proposed, but with no progress. This article studies the joint efforts made by the participating authorities in the SCS Workshop process to understand better the current state of marine biodiversity in the SCS.