The red coloring of pear fruits is mainly caused by anthocyanin accumulation.  Red sport, represented by the green pear cultivar ‘Bartlett’ (BL) and the red-skinned derivative ‘Max Red Bartlett’ (MRB), is an ideal material for studying the molecular mechanism of anthocyanin accumulation in pear.  Genetic analysis has previously revealed a quantitative trait locus (QTL) associated with red skin color in MRB.  However, the key gene in the QTL and the associated regulatory mechanism remain unknown.  In the present study, transcriptomic and methylomic analyses were performed using pear skin for comparisons between BL and MRB.  These analyses revealed differential PcHY5 DNA methylation levels between the two cultivars; MRB had lower PcHY5 methylation than BL during fruit development, and PcHY5 was more highly expressed in MRB than in BL.  These results indicated that PcHY5 is involved in the variations in skin color between BL and MRB.  We further used dual luciferase assays to verify that PcHY5 activates the promoters of the anthocyanin biosynthesis and transport genes PcUFGT, PcGST, PcMYB10 and PcMYB114, confirming that PcHY5 not only regulates anthocyanin biosynthesis but also anthocyanin transport.  Furthermore, we analyzed a key differentially methylated site between MRB and BL, and found that it was located in an intronic region of PcHY5.  The lower methylation levels in this PcHY5 intron in MRB were associated with red fruit color during development, whereas the higher methylation levels at the same site in BL were associated with green fruit color.  Based on the differential expression and methylation patterns in PcHY5 and gene functional verification, we hypothesize that PcHY5, which is regulated by methylation levels, affects anthocyanin biosynthesis and transport to cause the variations in skin color between BL and MRB.