Despite occupying less than 0.1% of the world's ocean surface, coral reefs are biodiversity hotspots and provide invaluable services to humankind. These precious ecosystems are severely threatened due to rapid anthropogenic climate change and overexploitation of natural resources. Through a combination of phylogenetic analyses, morphological measurements and population genetics, the ReeFISH project aims at understanding the ecological and evolutionary processes shaping fish biodiversity in coral reefs. Innovative methods will be used in this project, like a high quality underwater stereo-camera system to collect 3D morphological measurements of reef fishes. This data can be used to investigate the intra-specific morphological variations associated different habitats within coral reefs. This deeper understanding is a prerequisite to assess the potential impacts of ongoing and future changes on these taxa and to inform on best management practices of these ecosystems for the future.