Wide-compatibility varieties (WCVs), comprising a special class of rice germplasm, are able to produce fertile hybrids when crossed with both indica and japonica varieties. Dular, a landrace variety from India, has both a wide spectrum and high level of wide-compatibility when crossed with a range of indica and japonica varieties. In previous studies, an allele at the f5 locus from Dular (f5-Du) was identified as a neutral allele conferring wide-compatibility with a large effect on both pollen and spikelet fertility. Using a population of 1993 hybrid plants derived from a cross between ZS(f5-Du/f5-ZS) (F1 of near isogenic line of Zhenshan 97 containing f5-Du) and Balilla (a japonica tester), f5-Du was genetically mapped to an interval of about 1.6 cM, with 0.8 cM from both SSR markers WFPM3 and WFPR1. Combined with bioinformatic analysis, a contig map was constructed for the f5 region, consisting of five bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones and spanning approximately 437 kb in length. By assaying the recombinant events in the region with markers developed using the sequence information, the f5 locus was further narrowed down to a 70 kb fragment containing nine predicted genes. The result will be very useful for cloning this gene and marker-assisted transferring of the neutral allele in rice breeding programs.