Pathogenesis-related (PR) genes were isolated from chestnut rose (Rosa roxburghii Tratt) using a PCR approach with degenerate primers designed for the conserved regions of two PR gene families: class 2 (β-1,3-glucanase) and class 5 (osmotin). Thirteen PR2 and ten PR5 genes were obtained, with a nucleotide identity that ranged from 40.1 to 99.7% and from 99.2 to 99.8%, respectively. Sequence comparison revealed the presence of single nucleotide polymorphisms (SNPs) in these sequences with, on an average, one SNP in every 64-bp fragment for the PR2 genes and one in every 68-bp fragment for the PR5 genes. A total of 23 primers were used to genotype these SNPs for use in developing single nucleotide-amplified polymorphisms (SNAP) markers. One marker (Glu7) was found to be linked to powdery mildew resistance loci. Based on genetic mapping of a segregating F1 population, we determined that 16 of the 23 SNAP markers formed one group and subsequently detected a quantitative trait locus that accounted for 12% of the variation in the powdery mildew resistance phenotype. The results of this study provide a first insight into the genomic structure of PR genes and show that the candidate gene approach in combination with SNAP markers is an attractive strategy to search for powdery mildew resistance loci in chestnut rose.