Radiocarbon analyses, stable isotopic measurements and extensive field observations were made of coral reefs off the Pacific coast of Costa Rica and Panama. These analyses showed that live coral reefs in the Gulf of Papagayo, Costa Rica, were severely depleted in number, size and variety of species, compared to reefs in the major upwelling zone of the Gulf of Panama. Coral growth in the Gulf of Papagayo consisted mainly of dead reefs that died from 150–300 years B.P. The δ18O records revealed that most of the dead reefs were exposed to relatively cool water immediately preceding death. We propose that during the latter part of the Little Ice Age there was probably an equatorward shift of the Northern Trade Wind system, which caused an intensification of upwelling at lower latitudes. This increased upwelling was the likely cause of the demise of coral reefs in the Gulf of Papagayo.