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Dirigent (DIR) proteins mediate regio- and stereo-specific monolignol coupling during lignan formation (1), producing structurally diverse compounds that play a role in plant defense as antioxidants or biocides (2, 3). The Arabidopsis DIR family consists of 25 members, most of which have unknown physiological functions. DIR13 and DIR14 are the closest paralogs of DIR5 and DIR6, which participate in (-)-pinoresinol biosynthesis (4), as well as DIR12/DP1, which is essential for neolignan biosynthesis in seeds (5). However, DIR13 and DIR14 exhibit strong and preferential expression in the root (3, 4), but they lack the conserved residues necessary for (-)-pinoresinol formation (3). Using transcriptional fusion lines pDIR13::NLS:3XGFP, pDIR14::NLS:3XGFP, and pDIR14::GUS, we found that DIR13 and DIR14 are root-specific and active from the early stages of postembryonic growth. We observed that pDIR13 is strongly activated by cytokinins, particularly in the root tip. Detailed root histology, employing thin polyacrylamide sections of pDIR14::GUS roots, revealed that pDIR14 expression shifts from the procambium to meta- and protoxylem cells upon cytokinin induction. Protein fusions of DIR13 and DIR14 with mCherry showed their localization: DIR13 in the root endodermis and lateral root (LR)-forming basal cells, from LR primordia to mature LR, and DIR14 in the root vasculature. Analysis of overexpression and mutant lines indicates that DIR13 promotes LR growth and development. We also observed that DIR13 contributes to increased accumulation of reactive oxygen species (ROS) and (neo)lignans in roots. Furthermore, DIR13 enhances tolerance to salt stress during seed germination and reduces sensitivity to salt-induced inhibition of primary root elongation and LR growth. Application of progressive salt and drought stress to adult DIR13-overexpressing plants suggests that DIR13 positively regulates acclimation to abiotic stresses. Altogether, our findings reveal a new correlation between cytokinin signaling, (neo)lignan and ROS accumulation, and plant stress tolerance through DIR13 regulation.