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Coral reefs comprise a symbiotic system that coexists among ecosystems, landforms, and humans at various levels. Coral Reef Science aims to illuminate this complex system and to provide a scientific basis to reconstructing the symbiotic system coexisting between humans and coral reefs. The authors have conducted an interdisciplinary project Coral Reef Science from 2008 to 2012 and obtained novel results and a clue to unite different disciplines for a coral reef as a key ecosystem.