Forward and reverse genetics using the model legumes Lotus japonicus and Medicago truncatula have been instrumental for identifying the essential genes governing legume-rhizobial symbiosis. However, little is known about the effects of intraspecific variation on symbiotic signaling. Here, we use Quantitative Trait Locus sequencing (QTL-seq) to investigate the genetic basis of the differentiated phenotypic responses shown by the Lotus accessions Gifu and MG20 to inoculation with the Mesorhizobium loti exoU mutant that produces truncated exopolysaccharides. We identify the Pxy gene as a component of this differential exoU response through genetic complementation. Lotus Pxy encodes a leucine-rich repeat receptor-like kinase similar to Arabidopsis thaliana PXY, which regulates stem vascular development. We show that Lotus pxy insertion mutants display defects in root and stem vascular organization, as well as lateral root and nodule formation. Our work links Pxy to de novo organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that natural variation in Pxy affects nodulation signaling.