In this paper the current status of coral reefs, predictions concerning the ecological state of coral reefs to the 2025 time horizon and the research needs that can help understanding and management activities that might alleviate detrimental ecological changes are evaluated and discussed. The present rate of CO2 emissions will produce an atmospheric concentration in 100 years not experienced during the past 20 million years and water temperatures above those of the past interglacial 130 000 years before present. Human influences on water temperatures, seawater chemistry (toxic substances, nutrients and aragonite saturation), the spread of diseases, removal of species and food web alterations are presently changing reef ecology. A significant ecological reorganization is underway and changes include a reduction in calcifying and zooxanthellae-hosting organisms, their obligate symbionts, and species at higher trophic levels, with an increase in generalist species of low trophic level that are adapted to variable environments. Late-successional fleshy brown algae of low net productivity or non-commercial invertebrates such as sea urchins, starfish and coral-eating snails will dominate many reefs. These changes will be associated with a loss of both net benthic and fisheries production and inorganic carbonate deposition; this will reduce reef complexity, species richness, reef growth and increase shoreline erosion. To avert these changes management is needed at both global and local levels. Both levels need to reduce greenhouse gases and other waste emissions and renew efforts to improve resource management including restrictions on the use of resources and globalization of resource trade, run-off and waste production, and balancing potential reef production and resource consumption.