Cladocora caespitosa is the only reef-forming zooxanthellate scleractinian in the Mediterranean Sea. This endemic coral has suffered severe mortality events at different Mediterranean sites owing to anomalous summer heat waves related to global climate change. In this study, we assessed genetic structure and gene flow among four populations of this species in the Western Mediterranean Sea: Cape Palos (SE Spain), Cala Galdana (Balearic Islands), Columbretes Islands, and L’Ametlla (NE Spain). The results obtained from Bayesian approaches, FST statistics, and Bayesian analysis of migration rates suggest certain levels of genetic differentiation driven by high levels of selfrecruitment, a fact that is supported by egg-retention mechanisms. Conversely, genetic connectivity among distant populations, even if generally low, seems to be related to sporadic dispersal events through regional surface currents linked to the spawning period that occurs at the end of summer-beginning of autumn. These features, together with a certain isolation of the Columbretes Islands, could explain the regional genetic differentiation found among populations. These results help to better understand population structure and connectivity of the species and will serve as an approach for further studies on different aspects of the biology and ecology of C. caespitosa.