Fruit skin type is one of the most important components of fruit appearance. Pears have three types of fruit skin—russet, intermediate, and smooth—depending on the extent of the cork layer on the epicarp. Russet type is controlled by a dominant genetic factor, R, and a quantitative trait locus (QTL) associated with fruit skin type has been identified on chromosome 8. Although some markers have been developed, the relationship between their alleles and fruit skin type has not been established across multiple cultivars; thus, the effectiveness of these markers in marker-assisted selection (MAS) has not been demonstrated. In this study, haplotypes of 93 accessions estimated by Beagle 4.0 were classified into the major haplotypes HAP1–HAP8 using new simple sequence repeat (SSR) markers Psc07, Psc34, and Psc03. Out of the eight haplotypes, HAP1–HAP7 were found in Japanese pear, whereas HAP8 was specific to Chinese pear. By comparing the haplotypes and phenotypes of accessions and F1 populations, we found that HAP1–HAP3 and HAP7 had dominant effects and promoted cork layer formation, whereas HAP4–HAP6 and HAP8 were recessive and did not contribute to russeting. All eight haplotypes can be distinguished completely by Psc07 and Psc03, which would be useful for MAS. This information on haplotype structure of accessions and molecular markers associated with fruit skin type will be useful for future pear breeding programs.