AtPEPTIDE RECEPTOR2(AtPEPR2) is a member of leucine‐rich repeat receptor‐like kinase family and binds to a group of AtPROPEP gene‐encoded endogenous peptides,AtPeps. Previously, we found that AtPEPR2 plays a moderate role in the AtPep1‐mediated innate immunity responses in Arabidopsis leaf. In this study, we found that AtPEPR2promoter has strong activity in the vascular tissues of the roots and the atpepr2 mutants showed a moderate but significantly shorter root phenotype. AtPEPR2 partially mediated AtPep1‐induced root elongation inhibition. AtPep1‐triggered cytosolic Ca2ttransient rise in roots showed partial dependence on AtPEPR2 and fully on extracellular Ca2t([Ca2t]ext). Transcriptional profiling analysis found that expression of 75% of AtPep1‐modulated genes in roots was fully dependent on AtPEPR2, of which two dramatically induced genes showed partial dependence on the [Ca2t]ext.Arabidopsis genome contains seven Glutamine Dumpers genes(AtGDUs), encoding amino acid exporters. Three of them(AtGDU2, 3, 5) were among the top 10 genes that were downregulated by AtPep1 through AtPEPR2 fully dependent pathway. Treatment with AtPep1 strongly suppressed promoter activity of AtGDU3 in roots, which was relieved by chelating [Ca2t]ext. Arabidopsis overexpressing AtGDU3showed a shorter root phenotype and decreased sensitivity to the AtPep1‐mediated inhibition of root elongation. Taken together, this study demonstrated a significant role of AtPEPR2 in the AtPep1‐mediated signaling in the roots.