Coral reefs in Jakarta Bay have been subjected to scientific studies since the 1920s. Also from that time on biological collections were made. The reefs in the Jakarta Bay have been under long-term natural and anthropogenic stress. With the biological collections and historical documents the coral species richness in Jakarta Bay around 1920 was reconstructed. New data from this bay and the adjacent offshore Thousand Islands archipelago were obtained during a 2005 research expedition. A comparison of the coral assemblages between 1920 and 2005 reveals a clear decline in species numbers. The most prominent results include the near-shore disappearance of species belonging to the families Acroporidae, Milleporidae, and to a lesser extent Poritidae. The overall coral species composition of the reefs has changed considerably, which is partly reflected in a strong decline in coral species richness. About half the number of species recorded in 1920 was found again in 2005. (C) 2010 Elsevier Ltd. All rights reserved.