The present invention relates to a DNA fragment specific to a cytoplasmic male sterile pepper comprising a polynucleotide of SEQ ID NO: 1, a candidate polynucleotide (named orf456) associated with cytoplasmic male sterile pepper consisting of a 223.sup.rd to 678.sup.th nucleic acid of SEQ ID NO:1, and a polynucleotide of SEQ ID NO: 2. The DNA fragment specific to cytoplasmic male sterile pepper comprising a polynucleotide of SEQ ID NOs: 1 or 2 can be used for identifying cytoplasmic type between male sterile and male fertile pepper by the PCR method. In addition, hybrid pepper breeders/seed companies could detect impurities of the maintainer line within the CMS line, and by ensuring purity of the CMS line, a major source of contamination of the hybrid seeds is removed leading to obvious benefits for the seed industry and farmers.