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Giant clams obtain their nutrition from both filter-feeding and photosynthates produced by symbiotic zooxanthellae within their mantle tissue. The symbiotic partnerships between giant clam and zooxanthellae are critical for the health and survival of giant clams. Therefore, light/dark alternation plays a crucial role in influencing the growth performance and physiological change of the giant clam-zooxanthellae symbiosis in natural ecosystems. In this study, the rhythms of mantle surface area, physiological metabolic activity, and oxidative stress in the boring giant clam,
Tridacna crocea
, caused by two different light-dark cycles (7:00–19:00 light-on and 9:00–21:00 light-on, respectively) were investigated. The relative mantle surface area, net calcification rate and gross primary production significantly increased with the increase in light time, and the highest values were observed after 4–7 h of light exposure. The values of symbiosis Y (II) sharply increased when giant clams were transferred from dark to light conditions, and then slightly decreased to a low level until the next light/dark cycle. Dynamic changes of zooxanthellae density in the outer mantle were observed with two-peak values noted at 4 h after light-on and -off, respectively. The absorption of ammonium-nitrogen (negative values of ammonia metabolic rate) was observed when giant clams were exposed to light, and the rate reached its highest value after 10 h of light exposure. Rhythmic changes of oxidative stress related enzymes and antioxidant molecule were also detected in the inner and outer mantles. In detail, the highest values of SOD activity were observed around light-on time in both the inner and outer mantles, while the tendency of CAT activity was not the same in the inner and outer mantles; the GSH contents in the inner mantle were significantly higher than that in the outer mantle, and their values significantly increased with light exposure; the MDA concentrations from 5:00 to 14:00 were almost the same in both the inner and outer mantles, which were significantly higher than those at other sampling points. The rhythms of these detected behaviors and physiological responses were almost delayed with the delay of photocycle. This provides experimental support for the hypothesis that some behaviors and physiological responses of giant clams exhibit 24-h rhythms, which are affected by changes of light/dark alternation.