Coral reefs are major shallow-water ecosystems lining the coastlines of the tropical and subtropical belt. They have served the needs of human societies over the millennia, but are now experiencing unprecedented rates of degradation due to combined effects of anthropogenic impact and global climate change. An evolving global monitoring system draws on fundamentals of ecosystem structure and function, and on the continued advances in science and technology. Nevertheless, significant knowledge gaps remain, pertaining particularly to uncertainties in biological responses in the face of new, complex environmental challenges such as increasing temperature and ocean acidification, and how these are manifested in the broader ecosystem dynamics. In implementing a global programme, a major objective should be to engage the extensive network of developing country scientists, where the greatest concentrations of coral reef resources and the highest levels of species diversity are found. Success hinges on commitments by national governments, and on availability of sustained funding.