Current efforts to halt the decline of biodiversity are based primarily on protecting species richness. This narrow focus overlooks key components of biological diversity, particularly the infra-species genetic diversity, which is critical to consider with respect to genetic adaptation in changing environments. While comparative population genetics is recognized as a relevant approach to improve biodiversity management, it is still barely considered in practice. Here, a comparative population genetics study was conducted on two key habitat-forming octocoral species, Corallium rubrum and Paramuricea clavata , to contribute to management of two Marine Protected Areas (MPAs) in the northwestern Mediterranean. Contrasting patterns of genetic diversity and structure were observed in the two species, although they share many common biological features and live in similar habitats. Differential genetic drift effects induced by species-specific reproductive strategies and demographic histories most likely explain these differences. The translation of our results into management strategies supports the definition of four management units. We identified a coldspot of genetic diversity, with genetically isolated populations, and a hotspot of genetic diversity that has a central role in the system’s connectivity. Interestingly, they corresponded to the most recent and the oldest protected areas, respectively. This case study shows how moving from a “species pattern” perspective to an “eco-evolutionary processes” perspective can help assess and contribute to the effectiveness of biodiversity management plans.