Root rot is one of the most threatening diseases to pea production. Root rot is caused by several interacting soil-borne pathogens, which makes it challenging to manage. Breeding for resistance is a promising approach for sustainable pea production. While quantitative trait loci (QTL) for resistance against individual pathogens have been identified, the genetic basis underlying resistance against the pathogen complex is poorly understood. Using a previously described diverse panel of 254 pea genotypes and 18k single nucleotide polymorphism (SNP) markers, we identified a novel QTL for resistance to root rot on chromosome chr6LG2. This QTL co-locates with a mitochondrial Rho GTPase and an F-box gene model, which are promising candidates for disease control. A whole-genome prediction model explained up to 53% of the phenotypic variation and reached predictive abilities of up to 0.51 for root rot-related traits. We found that plant height and shoot biomass were unreliable plant health indicators. Instead, these traits were related to the Mendelian Le locus, which controls stem length. Our results provide new insights into the genetic basis of quantitative root rot resistance in pea and provide novel tools that could accelerate the development of resistant pea lines through marker-assisted and genomic selection.