The present study demonstrated that over-expression of copper-zinc superoxide dismutase (Cu/Zn-SOD), an important enzyme scavenging reactive oxygen species, improved vascular structures through lignification and imparted tolerance to salt stress (NaCl) in Arabidopsis thaliana (Arabidopsis; accession Col-0). Transgenic plants of Arabidopsis were developed by over-expressing cytosolic Cu/Zn-SOD from Potentilla atrosanguinea under CaMV35S promoter via Agrobacterium tumefaciens mediated transformation. Homozygous T(3) lines were analyzed for morphological, anatomical and molecular differences in response to salt stress. The transgenic plants showed higher germination and survival percentage, larger root length, larger rosette area and the higher number of leaves as compared to the wild type (WT) under NaCl stress. Anatomical studies of the inflorescence stem revealed significant thickening of inter-vesicular cambium in transgenics under NaCl stress as compared to the (i) WT and the transgenics raised in the absence of NaCl stress, as well as (ii) WT raised under NaCl stress. This thickening was possibly due to lignification as evidenced by the confocal microscopy. Also, the up-regulation of transcripts of critical genes of lignin biosynthesis, phenylalanine ammonia-lyase1 (PAL1) and peroxidase (PRXR9GE) in the transgenics supported lignification of vascular tissue under the above stated conditions. Results have been discussed on the possible implication of over-expression of PaSOD in lignification of vascular structure under NaCl stress in Arabidopsis.