Distribution and morphology of zooxanthellae were investigated histologically and ultrastructurally in veligers and juveniles of three giant clam species, Tridacna crocea, T. derassa, and T. squamosa. No zooxanthellal cells were associated with gametes. In veliger larvae, zooxanthellae were ingested and digested in the stomach. Within several days after metamorphosis from veliger to a juvenile clam, the zooxanthellal tube, in which zooxanthellae were packed, elongated from the stomach toward the mantle. Zooxanthellae in the tube appeared in a line, and we designated the appearance of the lined zooxanthellae in the mantle of juvenile clams as the first sign of the establishment of symbiosis. The zooxanthellal tubular system developed as the clams grew, particularly in the mantle margin, and then hypertrophied siphonal tissue formed. In zooxanthellal tubes, zooxanthellae usually had intact ultrastructures suggesting that they were photosynthetically active, while the stomach always contained degraded zooxanthellae that were probably discharged from the zooxanthellal tube. Giant clams probably digest zooxanthellae directly, and ingest the secreted photosynthates from zooxanthellae. There may be a selection mechanism to discharge unhealthy zooxanthellae from the mantle into the stomach. In addition to zooxanthellae, digested diatoms and other unidentified digested materials in the stomach suggest that filter-feeding also contributes to giant clam nutrition.