Crown rot, caused byPhytophthora cactorum, is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars (Fragaria×ananassaDuch) are generally susceptible, the diploid speciesFragaria vescais a potential source of resistance genes toP. cactorum. We previously reported severalF. vescagenotypes with varying degrees of resistance toP. cactorum. To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) ofF. vescawere analysed by RNA-Seq after wounding and subsequent inoculation withP. cactorum.Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response toP. cactorumafter wounding. These included putative disease resistance (R) genes encoding receptor-like proteins, receptor-like kinases, nucleotide-binding sites, leucine-rich repeat proteins, RPW8-type disease resistance proteins, and ‘pathogenesis-related protein 1’. Seven of theseR-genes were expressed only in the resistant genotypes and not in the susceptible genotype, and these appeared to be present only in the genomes of the resistant genotypes, as confirmed by PCR analysis. We previously reported a single major gene locusRPc-1(Resistance to Phytophthora cactorum 1) inF. vescathat contributed resistance toP. cactorum. Here, we report that 4–5% of the genes (35–38 of ca 800 genes) in theRPc-1locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation withP. cactorum. In particular, we identified three defence-related genes encoding wall-associated receptor-like kinase 3, receptor-like protein 12, and non-specific lipid-transfer protein 1-like that were highly expressed in the resistant genotypes compared to the susceptible one. The present study reports several novel candidate disease resistance genes that warrant further investigation for their role in plant defence againstP. cactorum.