Reef ecosystems are one of the most threatened environments on Earth. Because they provide invaluable services to coastal communities and sustain a large part of global biodiversity, the conservation of their biodiversity and functioning is vital. Millepora species are the second reef builders after scleractinians, yet little is known about them. Such foundation species, providing shelter, food and nurseries to thousands of species are essential to protect. The project “HydroReef” aims to characterize biodiversity and metapopulation dynamics of millepores through a multidisciplinary approach involving DNA barcoding, phylogeny, comparative phylogeography and population genetics on various spatiotemporal scales. DNA barcoding will accurately assess biodiversity in this problematic group. Phylogenetic reconstructions in light of geography and dating will reveal the drivers of speciation in the genus. Comparative phylogeography will help identify common evolutionary processes and biodiversity drivers among widespread Indo-Pacific species (e.g. barriers and refuges). A particular focus will be to identify past population size changes related to palaeoclimate variations. Population genetics using microsatellites and SNPs (genomic perspective) coupled to individual-based methods will provide estimates of ecological connectivity (DNA tracking of dispersal) and effective population sizes. The respective role of asexual and sexual reproductions on population persistence will be uncovered. This study will improve our understanding of some striking patterns of biodiversity (e.g. Indo-Australian-Archipelago biodiversity hotspot) and give an unprecedented view of millepore ecological functioning. It will provide information directly enhancing the protection and restoration of coral reefs. It will reveal regions of evolutionary importance and the spatial dimension of millepore connectivity, crucial information for both global scale conservation and design of Marine Protected Areas