Phytophthora sojae, the causal organism of stem and root rot, and Soybean mosaic virus (SMV) cause two of the most highly destructive diseases of soybean (Glycine max L. Merr). P. sojae can be managed either through deployment of race-specific resistance or through quantitative resistance termed partial resistance. In the current study, partial resistance to P. sojae was mapped in an interspecific recombinant inbred line (RIL) population of Glycine max by Glycine soja. One major quantitative trait loci (QTL) on molecular linkage group (MLG)-J (chromosome 16) and two minor QTL on MLG-I (chromosome 20) and -G (chromosome 18) were mapped using conventional molecular markers. Additionally, partial resistance to P. sojae was mapped in the same RIL population using single feature polymorphism (SFP) markers that further fine mapped the P. sojae QTL and identified potential candidate genes contributing to resistance. In a separate study, race-specific resistance was characterized in PI96983 discovering a potentially new allele of Rps4 on MLG-G. Finally, using the newly available whole-genome shotgun sequence of soybean, Rsv4 conferring resistance to strains of SMV known in the US, was localized to an approximately 100 kb region of sequence on chromosome 2 (MLG-D1B). Newly designed PCR-based markers permit for efficient selection of Rsv4 by breeding programs. Identified candidate genes for Rsv4 are discussed. Genomic resources developed in all of these studies provide breeders the tools necessary for developing durable resistance to both SMV and P. sojae.