Abstract The gonadotropin releasing hormone receptor (GnRHR) gene was studied as a candidate gene for the prolificacy of Small Tail Han sheep. Eight pairs of primers were designed to detect single nucleotide polymorphisms of exon 1, exon 2 and exon 3 of GnRHR gene in both high fecundity breeds (Small Tail Han and Hu sheep) and low fecundity breeds (South African Mutton Merino, Corriedale and Chinese Merino sheep) by PCR-SSCP. Only the products amplified by primers P4 and P7 displayed polymorphisms. For primer P4, two genotypes (AA and BB) were detected in Hu sheep, only one genotype AA was detected in other four sheep breeds. Sequencing revealed five mutations (+692G→A, +706T→A, +747T→C, +748A→T and +802T→A) of exon 1 in genotype BB compared with genotype AA, which gave rise to amino acid changes (Gly→Ser, Asp→Glu and Leu→Pro). For primer P7, two genotypes (CC and DD) were detected in prolific Small Tail Han and Hu sheep, only one genotype CC was detected in three low fecundity sheep breeds. Sequencing revealed two mutations (+50A→G and +101A→C) of exon 2 in genotype DD compared with genotype CC, which resulted in amino acid changes (Glu→Gly and Gln→Pro). In Small Tail Han sheep, frequency of CC and DD genotypes was 0.87 and 0.13, respectively. The Small Tail Han ewes with mutant homozygous genotype DD had 0.81 (P<0.01) lambs more than those with wild type CC.