In a context of biodiversity crisis, studying connectivity as well as specific and genetic diversities in fragmented ecosystems seems crucial to understand and predict their resilience ability. The oceanographic cruise MAD aimed to assess the genetic and specific diversities of marine populations from the North-East and the North-West regions of Madagascar. These regions are very rich in marine species diversity and present high endemism. The northwestern coast is adjacent to Glorieuses and Mayotte marine parks and the northeastern coast remains underexplored while very rich. To do so, we chose four benthic compartments: scleractinian corals, giant clams, macroalgae and holothurians, all presenting different ecosystemic functions and indicators of coral reef health. The MAD project aims to answer five main objectives: (1) achieve species inventories of giant clams, scleractinians, holothurians and macroalgae, in particular with tissue sampling for genetic analyses (molecular taxonomy and population genetics); (2) analyze the cryptic diversity of scleractinians corals (notably among Pocillopora genus); (3) implement national reference collections for corals and macroalgae; (4) complete the regional and indo-pacific sampling for some of the species; (5) assess the multi-scale genetic structures and the population connectivity for some of the species, sampled in the different islands of the Western Indian Ocean from other scientific programs.