We have used a red-fleshed apple cultivar, Malus ×domestica Pink Pearl, and its progeny, ‘JPP 35’, as paternal parents for producing new red-fleshed cultivars suitable for fresh use or processing such as pie fillings, dried apple, apple juice, or cider. In this process, we found that the S3-RNase allele of ‘Pink Pearl’ was linked to its red flesh trait. It was suggested that this trait might be controlled by a new gene apart from the MYB10 (MdMYB10) gene. Using ‘JPP 35’ (S-RNase allele genotype; S3S7) produced by ‘Jonathan’ (S7S9) × ‘Pink Pearl’ (S3Sx) as a paternal parent, we developed a system for producing red-fleshed progenies suitable for fresh use. That is, 96% and 86% of progenies from ‘Shinano Sweet’ (S1S7) × ‘JPP35’ (S3S7) and ‘Orin’ (S2S7) × ‘JPP35’ (S3S7) containing the S3-RNase allele, respectively, showed the red flesh trait. Similarly, red-fleshed progenies suitable for apple pie or natural red juice could be produced by ‘Jonathan’ (S7S9) × ‘JPP35’ (S3S7).