The red flesh in apple fruit is a desired trait by consumers and it is associated to the anthocyanin content, which is mainly controlled by MdMYB10 with a R6 promoter. In this study, a high-density linkage group was constructed using the ‘Fuji’ x ‘Red3’ population which contained homozygous alleles R1R1 and R6R6, respectively. The linkage group consists of 7630 SNPs along 17 linkage groups, spanning 2270.21 cM, with an average density of 0.30 cM per marker. The cyanidin-3-galactoside concentration was used as the phenotypic data in QTL analysis. Moreover, one QTL peak which was flaked by two markers, marker2187260 to marker2173766, with LOD scores of 4.49 was detected. This QTL ranged from 0 to 40.79 cM on the top of linkage group (LG16). In addition one candidate molecular marker (marker2175442) in this QTL was identified, which was significant correlated with the flesh cyanidin-3-galactoside concentration. These genetic findings enrich the breeding basis of fruit flesh coloration in apple.