Caspases have been demonstrated to possess important functions in apoptosis and immune system in vertebrate. But there is less information reported on the oyster larval development. In the present work, two full-length molluscan caspase genes, named Cacaspase-2 and Cacaspase-3, were characterized for the first time from Fujian oyster, Crassostrea angulata. Which respectively encode two predicted proteins both containing two caspase domains of p20 and p10 including the cysteine active site pentapeptide "QACRG" and the histidine active site signature. Otherwise Cacaspase-2 also contains a caspase recruitment domain. Homology and phylogenetic analysis showed that Cacaspase-2 shared high similarity with initiator caspase-2 groups, but Cacaspase-3 clustered together with executioner caspase-3 groups. Cacaspase-2 and Cacaspase-3 mRNA were both highly expressed in gills and labial palp and were significantly expressed highly in larvae during settlement and metamorphosis. Through the whole mount in situ hybridization, the location of Cacaspase-2 is in the foot of the oyster larvae and the location of Cacaspase-3 is in both the foot and velum tissues. These results implied that Cacaspase-2 and Cacaspase-3 genes play a key role in the loss of foot and Cacaspase-3 gene has an important function in the loss of velum during larvae metamorphosis in C. angulata.