Multiple subtypes of melatonin receptors are expressed in neural and peripheral tissues to mediate melatonin actions on the regulation of circadian rhythms in vertebrates. To elucidate molecular basis of "circa" rhythms in the grass puffer Takifugu niphobles, which spawns synchronously with semilunar cycles, tissue distribution of four melatonin receptor subtype mRNAs (Mel(1a) 1.4, Mel(1a) 1.7, Mel(1b), and Mel(1c)) were examined, and diurnal and circadian changes in their absolute amounts were examined in the retina, diencephalon, and optic tectum. Mel(1a) 1.4, Mel(1a) 1.7, and Mel(1b) mRNAs were widely distributed in various brain regions, retina, pituitary, and peripheral tissues, whereas Mel(1c) mRNA was mainly detected in the nervous tissues and pituitary. All subtype genes showed diurnal expressions with one or two peaks during nighttime. When the fish were reared under constant darkness, the retinal expressions of Mel(1a) 1.7, Mel(1b), and Mel(1c) genes were markedly diminished but still showed circadian variations. In contrast, increased and synchronized expressions of the four subtype genes were noticeable with one peak at circadian time 18 in the diencephalon. The circadian expression profiles in the optic tectum were different among the subtypes. The present results suggest that melatonin receptor gene expression is regulated by circadian clock and light, but the effects of light are different among the tissues. The synchronized expressions of the four subtype genes in the diencephalon may be related to the exertion of reproductive rhythmicity in this puffer species.