Reefs are of critical importance to human survival, providing subsistence food for a substantial portion of the population, serving as the principle coastal protection structures for most tropical islands, and contributing major income and foreign exchange earnings from tourism. According to a United Nations estimate, the total economic value of coral reefs range from US$ 100,000-600,000 km2yr-1. However, coral reef ecosystems worldwide are under threat from environmental and anthropogenic disturbances encompassing global climate change, storms, Crown-of-Thorns starfish outbreaks (COTS), sedimentation, pollution and unsustainable exploitation of reef resources. Such disturbances, while global phenomena, have largely been local in their effects. In 1998, however, unprecedented levels of coral bleaching indicated that global warming was likely to impact coral reefs at global scales, with the potential for simultaneous, large-scale impacts. The latest global climate change models predict continued warming and carbon dioxide increases, and with escalating threats from other human interventions, coral reefs are threatened worldwide. Unsustainable exploitation of Earth’s biological diversity has serious consequences for the goods and services that humans derive from coral reef ecosystems. Although biodiversity covers a multitude of scales, here our definition mainly focuses on species (i.e. species diversity) and their traits (i.e. functional diversity). Effective conservation of biodiversity is essential for human survival and the maintenance of ecosystem processes. In addition to its effects on the functioning of ecosystems, biodiversity influences the resilience and resistance of ecosystems to environmental change. Reductions in biodiversity due to environmental change can lead to a decrease in resilience (i.e the capacity of an ecosystem to tolerate disturbance without collapsing into a qualitatively different state that is controlled by a different set of processes). Therefore, if biodiversity is decreased, resilience is reduced and regime shifts are more likely. Regime shifts can in turn drastically affect ecosystems and the goods and services they provide. Understanding the capacity for biodiversity to persist or recover after disturbances, is crucial for devising appropriate management actions to mitigate biodiversity loss. Resilience to changes and potential regime shifts are complex phenomena, involving non-linearities and can be documented only once they have occurred. It is very difficult to predict them and determine which traits of the ecosystem determine resilience to multiple stressors. Long-term records are required in order to measure large-scale resilience from disturbances, but such records are scant, and there are thus few opportunities to study large-scale impacts and long-term recovery. Our project aims to resolve these problems. The need for sensitive metrics for evaluating resilience is of paramount importance and presents an ongoing challenge in coral reef management. Four factors have been proposed as critical in the maintenance of coral reef populations: i) recruitment, ii) zooxanthellae clades, iii) maintenance of grazing fish and benthic populations and iv) management of human activities. Our project is the first to consider all these factors in combination, assess those most important for biodiversity and determine the resilience of coral reefs in the face of multiple stressors.