Abstract Background Sheep’s reproductive physiology in temperate latitudes (such as Greece), is characterized by seasonality and is also regulated by photoperiodic exposure. Melatonin is the key hormone involved in this regulation. However, the melatonin secretion and therefore the ewes reproductive activity underlies variation, proposed to be linked with the melatonin receptor subtype 1A ( MNTR1A ) gene structure. This study was designed to investigate the polymorphism of the MNTR1A gene in a local Greek sheep breed and to determine its potential association with reproductive seasonality. Results Two groups of farmed ewes, each consisted of 30 individuals, were chosen. Males were introduced in both groups in spring (April). The first group consisted of ewes that showed reproductive activity in spring (May), while the second of ewes that showed reproductive activity 3 months later, in summer. The PCR–RFLP methodology was carried out on a 824-bp DNA fragment of the MTNR1A exon 2 using the Rsa I restriction endonuclease. The electrophoretic procedure revealed three genotypes, C/C , C/T and T/T . Specifically, 44 animals showed the C/C genotype (28 from the first group and 16 from the second), 14 the C/T genotype (2 from the first and 12 from the second) and 2 animals had the T/T genotype (both from the second group). Conclusions Statistical analysis indicated a positive correlation between genotype and reproductive seasonality, with C/C genotype playing a crucial role in out-of-season reproduction activity.