We used polymerase chain reaction (PCR) to clone the Carica papaya heat stress transcription factor gene, Cphsf. Phylogenetic analysis showed that Cphsf protein, named CphsfB1, is a homolog of Lycopersicon peruvianum HsfB1. Northern blot analysis revealed that CphsfB1 is constitutively expressed in radicles and is heat-inducible in leaves. The blast program embedded CphsfB1 in a gene cluster constituting four genes: accelerated cell death protein 2, abscisic acid 8'-hydroxylase, caltractin, and ethylene-responsive transcription factor. These results suggest that CphsfB1 has diverse roles in radicles and leaves, and may be related to seed germination. Polymorphic nucleotides in the 5' untranslated region of CphsfB1 were observed from a breeding material of TM1, but not in the cultivar 'Fruit tower'. Southern blot analysis showed two bands, 2.0 kbp (CphsfB1-2.0) and 2.3 kbp (CphsfB1-2.3), in TM1 and a single band, CphsfB1-2.3, in cv. 'Fruit tower'. The segregation ratio of CphsfB1-2.0 and CphsfB1-2.3 in F1 progeny derived from a cross between TM1 and cv. 'Fruit tower' fitted the expected Mendelian ratio of 1:1 (homozygote of CphsfB1-2.3:heterozygote). From the anther culture of TM1, six homozygotes each of CphsfB1-2.0 and CphsfB1-2.3 were produced. These results suggest that CphsfB1 is a single-locus gene, and CphsfB1-2.0 and CphsfB1-2.3 are alleles.