The influence of melatonin receptor 1A gene on litter size was studied in 150 ewes from Zel (n=100) and Naeini (n=50) sheep breeds. Two restriction fragment length polymorphism (RFLP) analyses were done to determine all genotypes occurring by variations at MnlI and RsaI restriction sites. The M and C were the most frequent alleles in both of these breeds. The MM genotype was predominant in Zel and Naeini breeds (0.52 and 0.60, respectively). The CT genotype (0.45) has the highest frequency in Zel and the CC genotype (0.44) was predominant in Naeini breed. The MMCT genotype was identified with the highest frequency of 0.25. There were no significant differences between melatonin receptor 1A (MTNR 1A) genotypes and litter size in Naeini ewes. But it seems that selection of animals with mm and Mm genotypes can progress mean litter size in Zel breed. The positive effect of mC and mT alleles was significant on lambing rate in Zel and Naeini breeds. However, the mmCT genotype has considerably greater mean litter size than the other ones. Finally, the MTNR 1A polymorphism can explain only a small part of the genetic variability on seasonal sexual activity between these breeds. Therefore, the implication of other genes must be noticed. Manuscript profile