Climate‐induced threats are increasingly affecting marine populations worldwide. In the last few decades, several gorgonian species have been affected by mass mortality events in the north‐west Mediterranean, putatively linked to local sea temperature increases during heatwaves. For many benthic sessile species, recovery after disturbances depends upon larval supply shaping the connections among populations. In the Ligurian Sea, genetic analyses showed that some Paramuricea clavata populations recovered after mass mortality events; however, the patterns of connectivity, and the potential role of migration in supporting the recovery of the populations of P. clavata, across its distribution range within the Ligurian Sea are still unknown. In this study, the population genetic structure and migration patterns of P. clavata populations have been analysed across seven sites in the Ligurian Sea, some of which have been affected by mass mortality events. Evidence of a population bottleneck was found in most of the populations studied. Significant genetic differentiation was found among P. clavata populations, reflecting habitat fragmentation at a regional scale, except for two populations found 20 km apart. Continuing gene flow between distant populations was also revealed. Empirical data suggest that gene flow among populations may have contributed to support their recovery from mass mortality events. The study identified populations in the central part of the Ligurian Sea that can be strategic for the regional persistence of the species. These findings highlight that the preservation of key populations could maintain connectivity and gene flow in the metapopulation, and increase the resilience of the species.