Phytophthora fruit rot is an important disease in eggplant. Identification of the disease-causing pathogens and the resistant germplasm accessions against these pathogens is useful in breeding of resistant varieties. In this study, the pathogens were isolated from the diseased eggplant fruit from Xuzhou city and Nanjing city of Jiangsu province, followed by tests for disease resistances in 146 globally-collected eggplant germplasm accessions. One strain was obtained from each of the samples in the two regions. Two strains (named NJ1 and XZ1) had typical characteristics of the phytophthora capsici, and both were P. capsici as revealed by rDNA-ITS sequence analysis. The eggplants post inoculation showed typical disease symptoms of phytophthora fruit rot. A variation on resistance among germplasm accessions was observed, and only several genotypes represented ideal resistance. Three germplasm accessions with ideal resistance to both strains could be used as a source of resistance for breeding eggplant against phytophthora fruit rot. Especially, G42 and G114 were resistant to both strains, while G135 was resistant to strain XZ1 and moderate resistant to strain NJ1. Collectively, this study has laid an important foundation for genetic breeding research on phytophthora fruit rot in eggplant.