The cDNA clone, CanMADS1, was isolated from young flower buds of the hot pepper (Capsicum annuum L.) by screening a cDNA library using the OsMADS1 rice MADS-box gene as a probe. We used a yeast two-hybrid screening method to investigate interaction partners of the protein product of CanMADS1. A MADS-box gene, CanMADS6, was isolated from young flower buds using the region containing the K domain and 15 amino acid residues of the C-terminal region of CanMADS1 as a bait. CanMADS1 and CanMADS6 showed high amino acid sequence similarities to members of the AGL2 subfamily and the SQUA subfamily, respectively. CanMADS1 transcript was expressed in flower buds and fruits, and the transcription signal was the strongest in the stage of the fruit set (2 d after anthesis). CanMADS6 showed the same expression pattern as CanMADS1. CanMADS1 and CanMADS6 were not expressed in leaves. These results suggest that a regulatory role for flower and fruit development of the hot pepper may be accomplished through an interaction of the protein products of the two MADS-box genes, CanMADS1 and CanMADS6.