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Jerboas are wild rodents exhibiting exceptional adaptation to their desert environment. Under harsh autumn conditions, they shut down reproduction, increase body weight and hibernate, while during spring they become sexually active even under negative energy-balance. We recently reported that these rhythms are associated with synchronized changes in genes expressing reproductive (Kiss1, Rfrp) and metabolic (Npy and Pomc) peptides, raising the hypothesis of coordinated seasonal regulation of both functions. Here we analyzed whether kisspeptin and RFRP-3 regulate food-intake in parallel to their established reproductive functions. Intracerebroventricular administration of kisspeptin inhibited food intake by 1.5-fold in fasted, but not ad-libitum fed, female jerboas captured in spring, an effect associated with an increase in Pomc and decrease in Rfrp mRNA levels. By contrast, intracerebroventricular injection of RFRP-3 induced a 4-fold increase in food-intake in ad-libitum female jerboas, together with a decrease in Pomc and increase in Npy mRNA levels. This orexigenic effect of RFRP-3 was observed in both spring and autumn, whereas kisspeptin’s anorexigenic effect was only observed in spring. Altogether, this study reports opposite metabolic effects of kisspeptin and RFRP-3 in the female jerboa and strengthens our hypothesis of a coordinated, season-dependent, regulation of reproductive activity and food intake through interactions of these hypothalamic peptides.