The wide compatibility gene, S 5 n , can overcome embryo sac sterility between indica and japonica subspecies of rice. Therefore, it is very important to characterize the features of the S 5 n sequence to reveal the origin and evolution of S 5 n . In this paper, 26 cultivated rice haplotypes and 22 wild rice accessions harboring S 5 n were used to sequence S 5 n . The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S 5 n sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710–1719 bp, including wild (O. nivara) and cultivated rice, such as IRW501 and Yuetai B. S 5 n sequences were not biased and evolved neutrally. The 48 materials could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice clustered into another group. Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found to lack 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S 5 n coding regions were crossed with testers (typically indica and japonica) to produced test cross F 1 populations. The F 1 s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S 5 n -containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, indirectly proving that S 5 n is a non-functional gene. The wide compatibility gene, S 5 n, can overcome embryo sac sterility between indica and japonica subspecies of rice. Thus, it is very important to characterize the features of the S 5 n sequence to reveal the origin and evolution of S 5 n. In This paper showed 26 cultivated rice haplotypes and 22 wild rice accessions harboring S 5 n were used to sequence S 5 n. The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S 5 n sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710-1719 bp, including wild (O. nivara) and cultivated rice, such as as The 48 papers could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found lack of 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S 5 n coding regions were crossed The F 1 s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S 5 n -containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, proving that S 5 n is a non-functional gene.