C-type lectin is a superfamily of Ca2+-dependent carbohydrate-recognition proteins that play significant roles in nonself-recognition and pathogen clearance. In the present study, a C-type lectin (PdC-Lectin) was chosen from stony coral Pocillopora damicornis to understand its recognition characteristics to zooxanthellae. PdC-Lectin protein contained a signal peptide and a carbohydrate-recognition domain with EPN motif in Ca2+-binding site 2. The PdC-Lectin recombinant protein was expressed and purified in vitro. The binding of PdC-Lectin protein to zooxanthellae was determined with western blotting method, and the bound protein to 10–105cell mL−1 zooxanthellae was detectable in a concentration-dependent manner. Less PdC-Lectin protein binding to zooxanthellae was observed for the incubation at 36°C than that at 26°C. Furthermore, the PAMP recognition spectrum of PdC-Lectin protein was tested through surface plasmon resonance method, and it bound to LPS and Lipid A, but not to LTA, β-glucan, mannose or Poly (I:C). When PdC-Lectin protein was preincubated with LPS, there was less protein binding to zooxanthellae compared with that in non-preincubation group. These results collectively suggest that PdC-Lectin could recognize zooxanthellae, and the recognition could be repressed by high temperature and pathogenic bacteria, which would help to further understand the molecular mechanism of coral bleaching and the establishment of coral-zooxanthella symbiosis in the stony coral P. damicornis.