Transcriptom Solexa sequencing was conducted on pepper early flower buds of the CMS line ‘9704A’ and its correspondence homonuclear maintainer line ‘9704B’ previously. A gene that expressed 10 times higher in pepper cytoplasm male sterile (CMS) line ‘9704A’ than it is in the maintainer line ‘9704B’ was identified. Gene homology analysis of the cloned hsf gene showed that the gene shares 87% homology with the hsf in Solanum lycopersicum, 73% in Vitis vinifera and 70% in Arabidopsis thaliana. According to the gene sequence we designed the primers and cloned the core sequence and hsf cDNA in pepper ‘9704A’. Sequence analysis showed that the cloned hsf cDNA was consistent with transcriptom Solexa sequencing. Gene analysis showed that the gene is one of the plants hsf gene family members. The real-time fluorescence quantitative RT-PCR primers were designed and the RT-PCR of the gene was carried out with the compared tissues in ‘9704A’ and ‘9704B’, using actin as reference gene. The result showed that the hsf gene expression in ‘9704A’ leaf is 13 times higher than it is in the maintainer line and in ‘9704A’ later flower bud is 3 times higher. The gene expressed very low in the stems of the two materials while high in the roots.