Melatonin has several known physiological functions, the main one being synchronization of daily and seasonal rhythms. In addition, melatonin has been reported to influence reproduction and behavioral rhythms with varying results depending on the species. To date, it remains unknown how this rhythm in locomotor activity is controlled endogenously, although there must be coordination of chemical and molecular drivers. However, the species is poorly characterized at molecular level with little sequence information available in public databases. The aim of study was to clarify involvement of endogenous melatonin rhythms and locomotor activity in day-night activity of the eel, Anguilla japonica which is an economically important but endangered species. The levels during daytime (zeitgeber time; ZT 6) were significantly (P<0.05) lower than those during nighttime (ZT 18). A similar pattern was persisted under DD conditions, whereas it disappeared under LL conditions and ocular melatonin levels remained low. Therefore, it is likely that ocular melatonin levels of the nocturnal eel reared under LD and DD conditions fluctuate in a daily/circadian manner and night-related physiological processes are dependent on eel locomotor activities which is a nocturnal species. We found that similar number of genes were differentially expressed between day (ZT6) and nighttime (ZT18), suggesting that during the nighttime also important in differential gene expression with daytime. This work also provides essential information for further studies investigating the molecular basis of daily/circadian system in this species.