Seasonally breeding animals use a combination of photic (i.e. day length) and nonphotic (e.g. food availability, temperature) cues to regulate their reproduction. How these environmental cues are integrated is not understood. To assess the potential role of two candidate neuropeptides, kisspeptin and RFamide-related peptide-3 (RFRP), we monitored regional changes in their gene expression in a seasonally breeding mammal exposed to moderate changes in photoperiod and food availability. Adult male Siberian hamsters (Phodopus sungorus) were housed under a long (16 h light/day; 16 L) or intermediate (13.5 L) photoperiod and fed ad lib. or a progressive food restriction schedule (FR; reduced to 80% of ad lib.) for 11 weeks. Gonadal regression occurred only in FR hamsters housed under 13.5 L. Immunohistochemistry was used to identify diencephalic populations of kisspeptin- and RFRP-immunoreactive cells, and quantitative PCR was used to measure gene expression in adjacent coronal brain sections. Photoperiod, but not food availability, altered RFRP mRNA expression in the dorsomedial sections, whereas food availability but not photoperiod altered Kiss1 expression in the arcuate sections; intermediate photoperiods elevated RFRP expression, and food restriction suppressed Kiss1 expression. Regional- and neuropeptide-specific activity of RFamides may provide a mechanism for integration of multi-modal environmental information in the seasonal control of reproduction.