Symbiotic dinoflagellates of the family Symbiodiniaceae play a fundamental role in shallow water coral physiology, ecology, and resilience to environmental change. Variations in symbiont composition can influence the response of host coral to thermal stress and other environmental stressors, making the characterization of coral-algal associations particularly relevant in the context of climate change. Despite their ecological importance, information on the large-scale distribution and composition of symbiotic algae in Mediterranean scleractinian corals remains limited. In this study, we assessed the genetic diversity of Symbiodiniaceae algae associated with two scleractinian species, namely Balanophyllia europaea and Cladocora caespitosa, using high-throughput sequencing of the Internal Transcribed Spacer 2 (ITS2) rDNA. A total of 204 coral samples were investigated across latitudinal and longitudinal gradients of environmental parameters at nine sites in the Mediterranean Sea, including Italy, France, and Cyprus. While B. europaea consistently harboured Philozoon dinoflagellate algae, colonies of C. caespitosa showed a major proportion of Philozoon ITS2 sequences at the western sampling sites and of Breviolum ITS2 sequences at the eastern sites. The potential roles of host species, site, and environmental conditions in shaping the coral-algal associations were tested via statistical analyses. Considering the ongoing warming of the Mediterranean Sea, this molecular characterization of coral-associated Symbiodiniaceae algae represents a baseline for comparisons with future trajectories. In addition, the results obtained in this study may have implications for restoration initiatives, with relevance for conservation and management strategies of the two investigated coral species.