Crown rot, caused by , is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars ( × Duch) are generally susceptible, the diploid species is a potential source of resistance genes to . We previously reported several genotypes with varying degrees of resistance to . To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) of were analysed by RNA-Seq after wounding and subsequent inoculation with Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response to after wounding. These included putative disease resistance () 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 these -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 locus () in that contributed resistance to . Here, we report that 4-5% of the genes (35-38 of ca 800 genes) in the locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation with . 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 against .