Phytophthora parasiticais one of the most widespread Phytophthora species, which is known to cause multiple diseases in tomato. Our current understanding of tomato-Phytophthora parasiticainteraction is very limited. In this study, we have analyzed and compared the transcriptome of a resistant and a susceptible wild tomato accession in response to P. parasitica infection using the RNA-seq technology. We have identified 2657 and 3079 differentially expressed genes (DEGs) in treatment vs control comparison of Sp-R and Sp-S samples respectively. Functional annotation of DEGs revealed substantial transcriptional reprogramming of diverse physiological and cellular processes particularly the biotic stress responses in both Sp-R and Sp-S upon P. parasiticatreatment. However, subtle expression differences among some core plant defense related genes were identified and their possible role in resistance development against P. parasiticais discussed. Our results revealed 1173 genes that were differentially expressed only in Sp-R accession upon P. parasiticainoculation. These exclusively found DEGs in Sp-R accession included some core plant defense genes for example, several protease inhibitors, chitinases, defensin, PR-1 etc. were all highly induced. Whereas, several R genes, WRKY transcriptions factors and a powdery mildew susceptibility gene (Mlo) were highly repressed during the resistance outcome. Analysis reported here lays out a strong foundation for future studies aimed at improving genetic resistance of tomato cultivars against to Phytopphthoraspecies.