Japanese pear (Pyrus pyrifolia) and quince (Cydonia oblonga), both classified in the subfamily Maloideae, show differences in inflorescence architectures despite of the fact that they are genetically closely related. We previously isolated flowering related genes, LEAFY (LFY) and TERMINAL FLOWER 1 (TFL1) homologues, from these species and showed that they had two types of homologues for each gene. In this study, we examined the expression pattern of LFY and TFL1 homologues in these species by in situ hybridization and RT-PCR. The floral bud was dissected to small pieces under stereomicroscope; apical meristem, scales/bracts, pith, floral meristem, and inflorescence; and then used for RT-PCR. The LFY homologues were expressed in apical meristem and scales/bracts before the floral differentiation in both Japanese pear and quince. After floral differentiation, the expression was observed in floral meristem, scales/bracts and pith in both the species. The TFL1 homologues were strongly expressed in the apical meristem, but their expression was drastically decreased just before floral differentiation. It is considered that the decrease of expression of TFL1 homologues is a sign of floral initiation. The expression of TFL1 homologues was transiently increased at the beginning of floral differentiation in both species. Moreover, one of TFL1 homologues in Japanese pear was continuously expressed in the inflorescence part in the floral primordia, whereas expression of TFL1 homologues in quince almost completely disappeared after a solitary floral meristem was initiated. It was suggested that TFL1 homologues may also be involved in the inflorescence development of Japanese pear.