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Phytophthora root and stem rot (PRSR) disease results in substantial losses in soybean production worldwide. The occurrence of PRSR caused by <i>Phytophthora sojae</i> Kaufmann & Gerdemann has become increasingly important for soybean production in the Republic of Korea, but domestic soybean–<i>P. sojae</i> interaction has been less studied. The disease has been managed by developing varieties harboring resistance to the <i>Phytophthora sojae</i> (<i>Rps</i>) gene. The present study aimed to identify a major gene locus conferring resistance to new <i>P. sojae</i> isolate 2858 in the recombinant inbred line population derived from a cross between parental lines ‘Daepung’ (susceptible) and ‘Saedanbaek’ (resistant). Seventy-three recombination inbred lines (RILs) were evaluated for resistance to <i>P. sojae</i> isolate 2858. A resistance locus was identified in the approximate 3.3–4.3 megabase pair region on chromosome 3 using both single-marker and linkage analyses. The <i>Rps</i> of Saedanbaek (<i>RpsSDB</i>) was located on the well-known <i>Rps</i> gene/allele cluster region, which also partially overlapped with a locus previously identified in the Korean soybean variety, ‘Daewon’, resistant to another <i>P. sojae</i> isolate 2457 (<i>RpsDW</i>). Approximately 402 kilobase pairs of the interval region overlapped, including six nucleotide-binding site-leucine-rich repeat (NBS-LRR)-coding genes. Additional phenotypic assays revealed that Saedanbaek was susceptible to isolate 2457 and that Daewon was susceptible to isolate 2858, indicating that <i>RpsSDB</i> and <i>RpsDW</i> are different genes or alleles that confer race-specific resistance to the two <i>P. sojae</i> isolates. These results provide information that will be helpful for breeders developing <i>P. sojae</i>-resistant cultivars.