The objective of this study was to identify quantitative trait loci (QTL) related to phytophthora root rot (PRR) tolerance and to analyze their genetic effects through two recombinant inbred line populations between tolerance cultivar Hefeng 25 and two susceptible cultivars (Dongnong 93046 for the HD population, including 140 F_5:9 lines, and Maple Arrow for the HM population, including 149 F_5:10 lines) based on greenhouse evaluation of PRR. A total of five and seven QTL underlying tolerance to PRR were identified in the HD and HM populations, respectively. Phenotypic variation explained by the QTL ranged from 1.27% to 10.41% in the HD population and from 1.68% to 12.65% in the HM population. Of these QTL, three (qHDPRR-4 in the HD population and qHMPRR-1 and qHMPRR-3 in the HM population) were identified in similar genomic regions reported previously. Nine new QTL contributed by Hefeng 25 were found in the present study (four in the HD population and five in the HM population). Three QTL in the HD and five QTL in the HM populations had higher additive effects that were likely to be stable across multiple environments or genetic backgrounds. Moreover, four and five epistatic pairwise QTL were found to underlie tolerance to PRR in the HD and HM populations, respectively.