The complex neuronal and hormonal interaction between the brain and gonads controls the neuroendocrine reproductive axis. GnRH, GnIH, and kisspeptin are important neuropeptides in this relationship. Although seasonal variations of these neuropeptides have been demonstrated in photoperiodic animals, there is no clear evidence in their daily rhythms. Melatonin and leptin hormones are also two important hormones in reproductive regulation. In our study, the relationship of melatonin and leptin hormones with daily rhythm with GnIH, GnRH, and kisspeptin gene expressions and protein oscillations was examined. Adult male Syrian hamsters were exposed to the long photoperiod and at the end of the 30-day experimental period, blood and tissue samples from each group were collected at 04:00 h, 12:00 h, 20:00 h, and 00:00 h. Daily rhythms of melatonin and leptin hormones were determined by ELISA. Quantitative analysis of GnRH, GnIH, Kisspeptin, and β-actin genes was performed with the corresponding primers in Real-Time PCR. Protein expressions were determined by the Western Blot technique. Serum melatonin and leptin levels showed an inverse rhythmic relationship. Leptin level was found to be low while melatonin was high in the dark. Daily rhythms were observed in GnIH, GnRH, and kisspeptin mRNA expressions and protein oscillations. As a result, our findings could imply that all of the relationships between melatonin, leptin, GnIH, GnRH, and kisspeptin are not reproductive, but rather metabolic in nature.