Giant clams are inhabitants of Indo-Pacific coral reefs. They commonly harbor three genera of phototrophic Symbiodiniaceae dinoflagellates (Symbiodinium, Cladocopium, and Durusdinium) as coccoid symbionts (zooxanthellae) mainly in the colorful outer mantle. Photosynthesizing symbionts release photosynthate that may include glycerol to the host. Hence, we cloned and characterized Glycerol Facilitator (GlpF) derived from the coccoid dinoflagellates in the colorful mantle of the giant clam, Tridacna squamosa, and reported herein three major GlpF cDNA sequences, one each for Symbiodinium, Cladocopium, and Durusdinium. The complete cDNA coding sequences of Symbiodinium-GlpF (Symb-GlpF), Cladocopium-GlpF (Clad-GlpF) and Durusdinium-GlpF (Duru-GlpF) comprised 1056, 1047 and 1029 bp, respectively. The respective deduced amino acid sequences consisted of 353 (36.9 kDa), 348 (36.5 kDa) and 342 (36.1 kDa) amino acids. All three encoded proteins had conserved residues associated with low water permeability and high glycerol selectivity, which are characteristics of aquaglyceroporin. Zooxanthellae-GlpF (Zoox-GlpF), which represented GlpFs of Symbiodinium, Cladocopium and Durusdinium phylotypes, was immunolocalized in some vesicles inside the symbionts. Some of these immunolabelled vesicles were located close to the symbiont's plasma membrane, parts of which also displayed immunofluorescence, indicating that these vesicles could probably release their contents through exocytosis. As illumination augmented the gene and protein expression levels of Zoox-GlpF/Zoox-GlpF in the outer mantle of T. squamosa, there could be an increase in the potential of glycerol transport through Zoox-GlpF in the coccoid dinoflagellates during photosynthesis. Future studies should examine whether different phylotypes of Symbiodinium, Cladocopium and Durusdinium would have dissimilar potentials of glycerol transport.