We isolated APETALA3 (AP3)-like and PISTILLATA (PI)-like cDNA clones called PaTM6 and PaPI from sweet cherry (Prunus avium). PaTM6 showed very high similarity to the TM6 lineage of AP3 of other Rosaceae species. PaTM6 contained three amino acid residues (F, T, M) within the MADS box and the (H/Q)YExM sequence near the K box, both of which are characteristic of the AP3 subfamily. A paleo AP3 motif was present at the C-terminal end of PaTM6. PaPI showed very high similarity to PI of other Rosaceae species. PaPI had the serine residue and the KHExL sequence within the MADS box and near the K box, respectively, both of which are characteristic of the PI subfamily. A PI motif was present at the C-terminal end of PaPI. Both PaTM6 and PaPI genes were expressed specifically in petals and stamens, the same expression patterns as those of class B MADS-box genes. These results indicated that PaTM6 and PaPI are homologues of AP3 and PI, respectively.