Bulked segregant analysis method was used to identify random amplified polymorphic DNA (RAPD) markers linked to the fertility restoring gene for the cytoplasmic male sterility (CMS) capsicum annum L. Totally 336 random primers were screened on the DNA samples of restorer and sterile bulks. Primer S418 produced a special band in restorer line. It was about 3000 bp, including two fragments 1515 bp and 1162 bp. Fluorescence in situ hybridization(FISH) indicated the fragment of 1515 bp only existed in restorer line.It was designed to S418(1515). Analysis of the sequence indicated S418(1515) was unknown before. The homology of blastn was less than 40%, however the homology of tBlastx indicated this sequence was high homologous with the part sequences of rice which were distributed on 2,4,7,10 chromosomes. It suggested this sequence might have the similar function with them. This result offered a good foundation to research the molecular mechanism of fertility restoration for CMS capsicum. Based on the sequence, special primers were designed to transform the RAPD marker to PCR marker. The result indicated that these primers could be used to screen the restorer lines from a large quantitive of candidate lines.