Flowering is a necessary condition and basis for yield in the life cycle of woody fruit trees.  Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain poorly characterized.  We identified genome-wide DNA methylation changes and the transcriptional responses in axillary buds of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasting flowering behaviors.  The DNA methylation levels were 19.35, 62.96 and 17.68% in FA, and 19.64, 62.49 and 17.86% in QA in the CG, CHG and CHH contexts, respectively.  The number of hypermethylated and hypomethylated differentially methylated regions (DMRs) in different regions contributed to significantly up- and downregulated gene expression.  DNA methylation can positively or negatively regulate gene expression depending on the CG, CHG and CHH contexts and their locations in different regions.  Additionally, the huge differences in transcription of MIKC^c-type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, aging, GA and sugar) by changing DNA methylation, contributed to contrasting flowering behaviors in both QA and FA.  Specifically, the floral meristem identity genes (i.e., FT, LEAFY, AP1 and SOC1) exhibited significantly higher expression in QA than FA, but the floral repressors (i.e., SVP, AGL15, and AGL18) showed the opposite trend.  Significant differences in multiple hormone levels were due to differentially expressed genes (DEGs) and their DMRs in hormone synthesis pathways, leading to both contrasting axillary bud outgrowth and flowering behaviors.  These findings reflect the diversity in the epigenetic regulation of gene expression and may be helpful for elucidating the epigenetic regulatory mechanism underlying the axillary bud flowering in apple.