Root and crown rot caused by Phytophthora capsici represents the main phytosanitary issue in pepper cultivation worldwide. Grafting is a widely adopted practice for soil-borne disease management. This research aimed to identify sources of resistance to P. capsici in accessions of Capsicum spp. through grafts. Six isolates from the province of Manabí, Ecuador were used, evaluating their aggressiveness by inoculation with P. capsici. Genetic resistance in 50 accessions of four species of Capsicum spp. and the resistance of susceptible grafts were evaluated in three genotypes as rootstocks along with the California Wonder variety as a susceptible scion. The results revealed variability in the aggressiveness of the isolates depending on the inoculation method, highlighting the high susceptibility in C. annuum and C. baccatum, while C. chinense and C. frutescens showed moderately resistant genotypes. A differential development of the disease was observed according to the combinations of scions and inoculations, highlighting the influence of the rootstocks on the resistance of the scions. The study addressed the aggressiveness of P. capsici isolates, the genetic resistance of different Capsicum species, the interaction between susceptible scions and selected rootstocks against the disease, and the identification of a P. capsici-resistant rootstock of C. frutescens. Resistant genotypes that can be used as rootstocks or sources of resistance in genetic improvement programs were produced; this information is valuable to understand and generate technologies that allow managing the incidence of Phytophthora capsici in crops of Capsicum spp.