Abstract:[Background] Favia favus is one of the main reef-building corals in the South China Sea, To our knowledge, to date no study has been performed on the symbiotic zooxanthellae in F. favus. [Objective] To investigate the phylogenetic diversity of the Symbiodinium in F. favus at different life stages, and to gain insights into potential acquisition mode of the Symbiodinium. [Methods] Fluorescence microscopy was used to detect the presence of symbiotic zooxanthellae in the eggs, larvae and adults of F. favus, respectively. Meanwhile, the clone library based on ITS2 sequence was constructed to assess the diversity of Symbiodinium. [Results] By means of direct examination with fluorescence microscopy, zooxanthellae was absent in the eggs and larvae but present in the adults of F. favus, which was assigned to Symbiodinium type C1 based on the ITS2 sequence analysis. [Conclusion] Only Symbiodinium type C1 was present in adults rather than eggs and larvae, suggesting that the symbiotic zooxanthellae in F. favus were probably acquired by horizontal transmission from the environment instead of vertical transmission.