Giant clams need to establish a symbiotic relationship with the microalgae Symbiodinium in the environment to survive the juvenile stage. In seed production of giant clams, larvae are presented with Symbiodinium but the probability of symbiosis establishment (symbiosis rate) is low. To determine the characteristics of Symbiodinium that improve the symbiosis rate of giant clams (Tridacna crocea and Tridacna maxima), we conducted experiments simulating a typical Japanese seed production method that rears giant clams in unsterilized seawater with no food or antibiotics. After validating this experimental method, we obtained the following results. First, the symbiosis rate was greater than O for Symbiodinium isolated from giant clams, corals, anemones, and even coastal seawater. It was slightly higher, albeit not significantly, for the giant clam origin Symbiodinium. Second, the symbiosis rate was sometimes better for cultured Symbiodinium than fresh Symbiodinium. In conclusion, Symbiodinium cultured after being isolated from giant clams can promote a symbiotic establishment of giant clam juveniles that are reared in unsterilized seawater with no food or antibiotics.