We have analyzed the promoter regions of MdMYB1 and 10 alleles in 8 apple (Malus x domestica Borkh.) cultivars and their progenies. The MdMYB1-1 allele responsible for red skin trait was identified in the red skin cultivars except for ‘Maypole’ and ‘Tomiko’. MdMYB10 (R6 type), MdMYB1-5 and MdMYB10 (R6 type), rather than MdMYB1-1, were identified in the red-skin, red-leaf and red-fleshed cultivars, ‘Maypole’ and ‘Tomiko’, respectively. It was suggested that their red-skin trait might be regulated by the MdMYB10 (R6 type) allele, which is responsible for red-leaf and red-flesh traits. Neither MdMYB1-1 nor MdMYB10 (R6 type) was identified in the green-leaf, yellow-skin, red-fleshed cultivar ‘Pink Pearl’, suggesting that its red-flesh trait might be regulated by some new allele or a gene other than MdMYB1-1 or 10 (R6 type). We identified 5 new MdMYB1 or 10 alleles, and MdMYB1 and MdMYB10 seemed to be a different allele since all cultivars and progenies investigated except for ‘Fuji’ contained only two MdMYB1 and 10 alleles.