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The recent advances in molecular ecology offer the opportunity to link evolutionary and conservation biology. Nevertheless, there is still a gap between evolutionary concepts and management policies. We present an overview of the molecular ecology studies conducted in the harvested red coral Corallium rubrum and how these studies may improve the species management. Due to its life history traits, its ecological role and the anthropogenic (overfishing) and climatic (mortality events) pressures impacting its populations, C. rubrum is an original model to characterize the interaction of evolutionary processes in the response of populations to global change. First population genetics studies demonstrated restricted gene flow among populations emphasizing the importance of local processes in population maintenance and suggesting strong population by environment interactions. Further studies based on microsatellites and RAD-sequencing thus aimed to characterize population functioning and reproductive biology and to look for imprint of local adaptation. The observed fine spatial scale genetic structure between colonies within a population implied that breeding units are restricted in space and composed by related individuals. We studied the interaction between population density and genetic drift in two populations differentially depleted by mortality events. The level of genetic drift was similar in the two populations suggesting that an increase of dispersal may balance to some point the decrease of population density. In order to characterize the impact of local adaptation in this species, we also developed integrative studies associating experimental, genetic (microsatellites and RAD-Seq) and transcriptomic approaches. We revealed a signal of local adaptation blurred by strong genetic drift, explaining potentially the differential mortalities observed during mortality events. A by-product of these genomic studies was the development of molecular sexing protocol. The implications for the management of red coral populations ranging from molecular forensic analyses, design of marine protected area to restoration actions will be discussed.