The population dynamics of zooxanthellae living in the mantle of a giant clam, Tridacna derasa, was studied. The giant clams with shell lengths of 5 to 6 cm which had been reared in the Palau Mariculture Demonstration Center, in the Republic of Palau, were transferred to aquaria on deck of the R.V. “Sohgen-maru” and kept in running sea water at 29 to 30 °C. Two clams were removed from the aquaria, and zooxanthellae in the mantle were isolated every 2 h for 24 h. Numbers of the zooxanthellae in or not in the cell division stage were counted for calculations of the zooxanthellae population in the mantle and their mitotic index (MI). The MI increased after sunset and reached the maximum values of 6.1 to 11.5% at 03:00 to 05:00 hrs. The specific growth rate, μ, estimated from the MI was 0.083 to 0.14 d−1. Five clams were kept in each of 2 Plexiglas containers in the aquarium for collection of the discharged feces every 3 to 4 h. The discharged zooxanthellae in the feces were counted. The zooxanthellae discharged in 24 h were 0.38 to 1.46% of the total zooxanthella population in the mantle, and 2.7 to 16.9% of the newly formed zooxanthella population in a day. Increase of zooxanthella population in the mantle was estimated from clam shell growth rate and from the correlation between zooxanthella population and clam shell size. Daily increase of zooxanthella population in the mantle was estimated to be approximately 7.6 to 19% of the newly formed zooxanthella population. Therefore, the sum of zooxanthellae populations accounting for daily increase in the mantle and discharge in the feces was 11 to 36% of the newly formed population. About 64 to 89% of the newly formed cells were missing; some of these may have been digested by the clam.