Enhanced cell wall lignification is one of the major salinity tolerance strategies in the roots of halophytes. A deep insight into the exact root developmental system in halophytes may be of great importance for understanding plant salt tolerance mechanisms. In this work the developmental and anatomical changes in the roots of halophyte Aeluropus littoralis along with expression patterns of two genes encoding for cell wall laccase (LAC4) and peroxidase (PER64) were investigated. The plants were treated with 0, 300 and 600mM NaCl and root samples were collected 3, 6 and 9days after treatment (DAT). Upon salinity treatment, root diameter and parenchyma thickness were increased significantly in the tip and middle segments compared to upper zones, but the change trend was reversed with the time. It was interestingly revealed that protoxylem was the tissue of target for lignification at root tips, while the highest lignification rates were observed in metaxylem and endodermis in upper segments. Compared to endodermis, protoxylem is restrictively involved in early stages of salt stress in root tips as an efficient barrier against Na+ flow. Gene expression analysis revealed that LAC4 expression was higher in root tips resulting in enhanced protoxylem lignification while PER64 expression was higher in more differentiated zones leading to endodermis thickening. The overall results of this study reveal the crucial role of LAC4 as an important gene in specialized protoxylem lignification in undifferentiated root tips leading to enhanced tolerance in early stages of salt stress.