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Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify <i>RpsX</i> in soybean cultivar Xiu94-11 resistance to all <i>P. sojae</i> isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed <i>RpsX</i> was located in the 242-kb genomic region spanning the <i>RpsQ</i> locus. However, a phylogenetic investigation indicated Xiu94-11 carrying <i>RpsX</i> is distantly related to the cultivars containing <i>RpsQ</i>, implying <i>RpsX</i> and <i>RpsQ</i> have different origins. An examination of candidate genes revealed <i>RpsX</i> and <i>RpsQ</i> share common nonsynonymous SNP and a 144-bp insertion in the <i>Glyma.03g027200</i> sequence encoding a leucine-rich repeat (LRR) region. <i>Glyma.03g027200</i> was considered to be the likely candidate gene of <i>RpsQ</i> and <i>RpsX</i>. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the <i>RpsX</i> and <i>RpsQ</i> alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.