ABSTRACT. The heat-shock transcription factor (Hsf) gene CaHsfA2 (GenBank accession No. JX402923) was cloned from the Capsicum annuum thermotolerant line R9 by combining the techniques electron cloning and rapid amplification of cDNA ends. The gene, which is 1436 bp in length, had an open reading frame of 1089 bp that encoded 362 amino acids. There was an 831-bp intron between positions 321 and 322 of the cDNA. The deduced amino acid sequence of CaHsfA2 contained the conserved domains of Hsf, including DNA binding domain, adjacent domain with heptad hydrophobic repeats (A/B), activator motifs, nuclear localization signal, and nuclear export signal, and it had the highest E value of hypothesized annotation of HsfA2. CaHsfA2 had the nearest phylogenetic relationship with HsfA2 from Lycopersicon peruvianum and Mimulus guttatus, which was consistent with its botanical classification. After heat-shock treatment at 40°C for 2 h, the expression of CaHsfA2 was observed in different tissues of thermotolerant cultivar R9 and thermosensitive line B6; however, the expression levels of the CaHsfA2 gene were significantly different as follows: expression in B6 leaf > stem > flower > root, and expression in R9 flower > leaf > stem ≈ root.