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Southern stem canker (SSC) in soybean [Glycine max (L.) Merrill], caused by the fungal pathogen Diaporthe aspalathi, is a major disease in the southern United States. It can cause up to 80% yield loss in severely infected fields. Plant introduction (PI) 398469, a Maturity Group VI soybean accession from South Korea, is one of six known sources of resistance to SSC. To determine the genetics of the resistance provided by PI 398469, F2:3 and F5‐derived recombinant inbred line (RIL) populations were developed from a cross with the susceptible breeding line G81‐2057. Both populations were phenotyped in the greenhouse using a modified toothpick method. The SSC‐resistant and susceptible DNA bulks consisting of 20 resistant and 18 susceptible families were created from the F2:3 population and genotyped using the Infinium SoySNP50K BeadChips for a bulked segregant analysis (BSA). Based on BSA results, 22 Kompetitive allele specific polymerase chain reaction (KASP) markers were designed to genotype the RIL population. Quantitative trait locus (QTL) analysis identified qRdm_14, on chromosome (Chr) 14 with an R2 of 62%. Linkage mapping in the F2:3 population confirmed the presence of a QTL on Chr 14. F5‐derived RILs derived from G81‐2057 × Crockett were phenotyped for SSC resistance and genotyped with the KASP markers to examine the relationship between Rdm3 from Crockett and qRdm_14 from PI 398469. Both PI 398469 and Crockett carried realleles at the Rdm3 locus for resistance to SSC. The QTL and KASP marker information could be used to screen breeding lines for resistance to SSC. Core Ideas: Resistance to soybean southern stem canker is provided by a major QTL on chromosome 14 from PI 398469.Both PI 398469 and Crockett carry resistance alleles at the Rdm3 locus on chromosome 14 for SSC resistance.KASP markers developed for the Rdm3 locus can be used by breeders to perform marker‐assisted selection. [ABSTRACT FROM AUTHOR]