Two apple [Malus sylvestris (L.) Mill. var. domestica (Borkh.) Mansf.] homologous fragments of FLO/LFY and SQUA/AP1 (AFL and MdAP1, respectively) were analyzed to determine the relationship between floral bud formation and floral gene expression in `Jonathan' apple. The AFL gene was expressed in reproductive and vegetative organs. By contrast, the MdAP1 gene, identified as MdMADS5, which is classified into the AP1 group, was expressed specifically in sepals concurrent with sepal formation. Based on these results, AFL may be involved in floral induction to a greater degree than MdAP1 since AFL transcription increased ≈2 months earlier than MdAP1. Characterization of AFL and MdAP1 should advance the understanding of the processes of floral initiation and flower development in woody plants, especially in fruit trees like apple.