The red color of apples (Malus domestica) is an attractive trait for consumers. The green skinned “Granny Smith” cultivar develops red pigmentation after bagging treatment. DNA methylation plays an important role in various developmental processes in plants. To explore the possible functions of DNA methylation in the pigmentation of bagged “Granny Smith” apples, we first analyzed the anthocyanin content of fruit skin following treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC). The results revealed an increase in anthocyanin content in bagged fruits following 5-aza-dC treatment, while no anthocyanins were detected in unbagged fruits. In addition, 8482 differentially expressed genes between 5-aza-dC-treated and control groups were identified in bagged fruits by RNA sequencing, including genes encoding transcription factors, enzymes related to anthocyanin accumulation, and methylases. Changes in the expression of these genes may be responsible for 5-aza-dC-induced red pigmentation in bagged fruits of “Granny Smith”. The findings provide novel evidence for the involvement of DNA methylation in the red pigmentation of non-red-skinned apples.