In cnidarians, the enzyme carbonic anhydrase (CA) is important to inorganic carbon (Ci) flux in processes including calcification and dinoflagellate symbiont photosynthesis. Although CA is known to function in Ci delivery to symbionts in adults with mature symbioses, it is not known when CA becomes active in this capacity during the onset of symbiosis in developing hosts. We identified two CA cDNA sequences from the planula larvae of the Hawaiian scleractinian coral Fungia scutaria. Expression of these larval CAs did not differ between infected and uninfected larvae or vary over the course of infection. Bioinformatic analyses of the two homologs showed that the sequences are unusually short and are missing some residues that support active site structure in other CAs. This is the first description of a short form of CA. Phylogenetic analyses of the larval CAs grouped them with membrane-bound homologs from vertebrates. Studies in other calcifying cnidarians have identified membrane-associated CAs as functioning in calcification, and therefore the two larval CAs could play a role in the onset of calcification during metamorphosis. A longer CA isoform was amplified from adult F. scutaria cDNA but not from larvae, suggesting that the longer form is not expressed in larvae. The longer form grouped with cytosolic CAs including a symbiotic anemone homolog implicated in Ci delivery to dinoflagellate symbionts. The apparent absence of this "symbiosis" CA in larvae suggests that the Ci supply mechanism is not active during the initial onset of the association.