Oryza rufipogon exhibits abundant genetic diversity and contains many elite genes. In this work, a total of 441 accessions of O. rufipogon were genetically examined using the functional marker S5n, revealing that 18 accessions carried the S5n allele with a heterozygous genotype (S5nS5i/j). Of these accessions, 14 were from Guangdong Province, 2 from Guangxi Zhuang Autonomous Region, 1 from Hainan Province and 1 from Jiangxi Province. Further sequence analysis spanning both sides of the deletion in S5n allele of O. rufipogon confirmed that this allele is identical with that of 02428, a wide-compatibility variety of domesticated rice. The segregation ratio of the 3 genotypes (S5iS5i/S5jS5j:S5nS5i/j:S5nS5n) among 15 self-bred progenies of O. rufipogon significantly deviated from the Mendelian expectation (1:2:1) in that the proportion of plants exhibiting S5n heterozygous and homozygous genotypes was much lower in the progeny. Sequence analysis of full-length S5n alleles indicated that a few base pairs were different between O. rufipogon and O. sativa, and it was presumed that S5n may be an ancient allele. The fertility of the embryo sac in plants with an S5n heterozygous genotype was low, suggesting the existence of other genes controlling embryo sac fertility in the wild rice. Oryza rufipogon exhibits abundant genetic diversity and contains many elite genes. In this work, a total of 441 accessions of O. rufipogon were genetically examined using the functional marker S5n, revealing that 18 accessions carried the S5n allele with a heterozygous genotype (S5nS5i / j ). These accessions, 14 were from Guangdong Province, 2 from Guangxi Zhuang Autonomous Region, 1 from Hainan Province and 1 from Jiangxi Province. Further sequence analysis spanning both sides of the deletion in S5n allele of O. rufipogon confirmed that this allele is The segregation ratio of the 3 genotypes (S5iS5i / S5jS5j: S5nS5i / j: S5nS5n) among 15 self-bred progenies of O. rufipogon significantly deviated from the Mendelian expectation ( 1: 2: 1) in that the proportion of plants exhibiting S5n heterozygous and homozygous genotypes was much lower in the progeny. Sequence analysis of full-length S5n alleles indicated that a few fertility of the embryo sac in plants with an S5n heterozygous genotype was low, suggesting the existence of other genes controlling embryo sac fertility in the wild rice.