Abstract: To analyze the structure and function of the melatonin 1b receptor (MT2) in sheep, single nucleotide polymorphisms were detected in exon 2 of sheep MT2 gene using genomic DNA from five sheep breeds by five primers. Polymorphisms were found, and 33 nucleotide mutations were revealed by comparing the mutant types with the wild types. Among them, 14 give rise to deduced amino acid changes. However, none is likely to be associated with nonseasonal or seasonal estrus in sheep breeds tested. Sequence of exon 2 of MT2 of Small Tail Han sheep shows much closer phylogenetic relationship with predicted bovine and porcine MT2 than with human and mouse. The deduced amino acid sequence shows higher identity with the MT2 of cattle (95%) and pig (79%) than with human (76%) and mouse (71%). A rather high identity (61–63%) with the MT1 of sheep, human and mouse was also found. Compared with the other known MT2, 35 unique altered amino acids were revealed. Albeit it also contains a NAXXY motif in transmembrane 7, both a DRY motif and a CYVCR motif were detected just downstream from its third transmembrane domain rather than NRY and CYICH found in other melatonin receptor groups. We presumed that it is possible that the structural changes make its binding function to the ligands attenuated or disrupted, and other genes (most probably MT1) were substituted in the progress of evolution, which ultimately resulted in no detectable expression in current breeds of sheep.