Driven by the low affinity to substrate possessed by RuBisCO, photosynthetic organisms have evolved Carbon Concentration Mechanism (CCM) to enrich the CO₂ concentration in the cell compartment to facilitate photosynthesis. Carbonic anhydrases (CA) are the key enzymes of CCM that catalyze the interconversion between CO₂ and HCO₃^-. However, we know little about the CCM of dinoflagellate at cellular level, and CA types still remaine to be elucidated. Dinoflagellates Symbiodiniaceae live in symbiosis with cnidarian, providing host cells with photosynthate synthesized from the inorganic carbon from host cell, is crucial to the coral-algae symbiont. In this study, we make the first attempt to classify the multi-types of CAs of Symbiodiniaceae. Four classes CA(αï¼?beta;ï¼?gamma;ï¼?delta;-CA) enconded gene were identified and classified in Symbiodiniaceae by data mining and phylogenetic analysis. Full length δ-CA coding gene was identified in Fugacium kawagutii, and the predicted subcellular localization and protein structure was investigated as well. By searching public transcriptomic datasets of Symbiodiniaceae, we summarized different gene transcript expression pattern of different CA genes under various growth conditions. The result shows that CA transcript expression is affected by nutrient limitation and elevated temperature. This study lays a foundation to further address the mechanism of inorganic carbon exchange in symbiont and provides a new perspective for understanding the formation and maintenance of coral-algae symbiosis.