Changes of endogenous 9, 10-ketol-octadecadienoic acid (KODA) concentrations, which is synthesized from linolenic acid by 9-lipoxygenase, were analyzed in apple [Malus ×sylvestris (L.) Mill. var. domestica (Borkh.) Mansf.] buds. In addition, the effects of 15, 16-chloro, hydroxy-9-hydroxy-10-oxo-12(Z)-octadecenoic acid (CKODA) application, which is an analog of KODA, on flower bud formation and the expression of MdTFL1 (terminal flower 1) and MdFT1 (flowering locus t 1) genes in apple buds were investigated in heavy-crop treatment (HCT) and under shade. An increase of endogenous KODA in the buds in the fruit-thinning treatment, which resulted in a higher proportion of flower bud formation than in HCT, was observed at 63 days after full bloom, but no such increase was found in HCT. In the shade-treated and heavy-crop trees, the expression of MdTFL1 in the buds to which CKODA was applied was lower than that in untreated buds. In contrast, under shade, the expression of MdFT1 in the CKODA-treated buds was higher than that in untreated buds. These results suggest that endogenous KODA may be associated with flower bud formation, and its application may be effective at improving the proportion of flower bud formation through its effect on MdTFL1 and MdFT1.