Photoperiod plays a role in controlling the initiation and termination of reproduction in fish. Melatonin is an internal transducer of environmental photoperiod and is involved in regulating reproduction. The present study aimed to examine how melatonin impacts the transcript levels of kisspeptin ( kiss1 and kiss2 ), gonadotropin-releasing hormones ( gnrh1 ), and the β -subunit of gonadotropins ( fshβ and lhβ ) in the brain of the sapphire devil, a tropical damselfish with long photoperiod preference. Feeding mature females with melatonin-containing pellets inhibited increases in the transcript levels of kiss1 , gnrh1 , and lhβ within 3 h. Continuous melatonin treatment for 1 week resulted in oocyte regression and downregulation of kiss2 , gnrh1 , fshβ , and lhβ . When the transcript levels of kiss1 and gnrh1 were measured at 4-h intervals in the brain of sapphire devil, a day–low/night–high fluctuation was observed. The hypothalamic– pituitary–gonadal (HPG) axis may be influenced by melatonin, exerting a negative effect at night because the transcript levels of aralkylamine N -acetyltransferase ( aanat2 ) increased during the scotophase. The expression of aanat2 was higher under short-day than long-day conditions, suggesting that there is a seasonal change in melatonin levels at night. It was concluded that change in photoperiod becomes a proximal factor for controlling the hormone synthesis in the HPG axis through melatonin.