Using clock genes in the yellowtail clownfish Amphiprion clarkii, we investigated the effects of light spectra and melatonin on circadian rhythms using light-emitting diodes (LEDs): red, green, and blue. To assess differences in circadian rhythms under different LED light spectra, we measured changes in the expressions of Melatonin receptor 1 (MT1) and Period 2 (Per2) and Cryptochrome 1 (Cry1) genes and changes in the plasma melatonin levels. Under red light, MT1 expression was significantly higher than that under other light spectra, but Per2 and Cry1 expressions were significantly lower than were those under other light spectra. Plasma glucose was significantly higher under red light than under other light spectra. These results indicate that, because red light is rapidly absorbed by water molecules, it cannot be detected by fish and acts as a stressor. In addition, melatonin regulates circadian rhythms via clock genes, and green and blue lights may be the most suitable for altering circadian rhythms in yellowtail clownfish, as these wavelengths generally penetrate seawater more efficiently than that by red light.