The level and pattern of nucleotide variation in the SUPERWOMAN1(SPW1) locus of the wild rice Oriza rufipogon and its related species were analyzed. SPW1 is orthologous to APETELA3(AP3) in Arabidopsis thaliana. The estimated level of nucleotide variation for the entire region (π = 0.0046) was intermediate among those for other genes of O. rufipogon, although the estimates varied considerably among the SPW1 domains. Complicated haplotype structure was detected, resulting in a high proportion of significant linkage disequilibrium. Deviation from the neutrality was not detected. However, purifying selection was suggested by lack of replacement variation in the MADS-box and I-domain regions, which function as DNA-binding domain. On the other hand, an excess of drastic amino acid changes was detected in the C-domain, as in the AP3 region of A. thaliana. Taken together, these results imply that different types of natural selection are acting among different domains of a single protein. In the phylogenetic tree, O. sativa strains were included in the same cluster of O. rufipogon, supporting the hypothesis that O. rufipogon is the wild ancestor of O. sativa.