Coral reefs are the planet's most diverse marine ecosystem, with the highest standing biomass, and the most species of fishes. Coral reefs are crucial to tropical ocean functions and to the human populations utilising the natural resources in these regions. Yet many of these complex ecosystems are threatened by impacts ranging from losses of essential habitats, to extinction risks for marine species. Furthermore, the long term effects of anthropogenic impacts, including global climate change exacerbate these stresses to the marine environment. The degradation of coral reef communities and their subsequent rates of recovery are important early-warning indicators of local and global marine ecosystem health. The need for long-term monitoring of coral reefs in a relatively natural state, to establish benchmarks for measuring changes and recovery in impacted reef systems, has been recognised, but there are few anthropogenically unaltered sites to study. Aldabra Atoll is one such site.

The Aldabra Marine Programme was formed in 1999 with a primary goal to establish the first permanent underwater survey sites for long-term, quantitative studies at Aldabra. Many studies of the effects of coral bleaching had documented the collapse of reef structure and degradation of the reef into algal-dominated systems, with the concomitant changes in reef fishes. The AMP studies would determine the ability of coral reef systems to replenish lost coral populations, reinstate framework growth, and recover reef habitat structural complexity and reef fish communities.