The cytoplasmic male sterility for wild-abortive (CMS-WA) has been wildly used for hybrid rice breeding in China. The fertility restoration of CMS-WA is controlled mainly by two independent and dominant nuclear fertility restoring genes, Rf-3 and Rf-4. To map the Rf-4 gene with molecular markers, rice YAC clones of RGP, Japan were used to create new molecular marker. YAC contigs located between RFLP markers R1877 and G2155 on chromosome 10 were confirmed by hybridization with 12 RFLP probes. Six YAC clones, Y4630, Y2670, Y4892, Y2111, Y3821 and Y5528 were identified. Chromosome DNAs of the YAC clones were prepared and separated by CHEF. A total of 119 probes were created by sub-cloning of the YAC DNAs. RFLPs were screened between Zhenshan 97A and its near-isogenic lines with Rf-4Rf-4 genotype. Two probes, Y3-8 from Y4892 and Y1-10 from Y4630, were found to be polymorphic. Using F2 populations from crosses between Zhenshan 97A and its near-isogenic lines ZSR11, Y3-8 and Y1-10 were mapped to Rf-4 locus with genetic distances of 0.9 cM and 3.2 cM, respectively.