In seasonal species, the photoperiod (i.e. day length) tightly regulates reproduction to ensure that birth occurs at the most favourable time of year. In mammals, a distinct photoneuroendocrine circuit controls this process via the pineal hormone melatonin. This hormone is responsible for the seasonal timing of reproduction, but the anatomical substrates and the cellular mechanisms through which melatonin modulates seasonal functions remain imprecise. Recently, several genes have been identified as being regulated by the photoperiod in the brain of seasonal mammals. These genes are thought to play active roles in the regulation of seasonal biology, notably for the adjustment of reproduction and body weight. Here, we briefly review findings associated with the control of seasonal breeding and describe recent data ascribing photoperiodic roles to type 2 and type 3 deiodinases, to the Kiss1/GPR54 system and to the RFamide-related peptides.Interestingly, these systems involve different hypothalamic nuclei, suggesting that several brain loci may be crucial for melatonin to regulate reproduction, and thus represent key starting points to identify the long-sought-after mode and site(s) of action of melatonin. Such findings raise great hopes for the future and could herald a new era of research in the field of seasonal biology.