United Nations predicted forthcoming food scarcity creates an urgency in research to assess and improve agriculturally important plant yield under environmental stress conditions. In this context, lignans are potential defensive substances that accumulate in plants during abiotic stresses. Flax (Linum usitatissimumL.) is one of the richest lignan source. Plant genotypes differ in lignan contents. Therefore, to draw a correlation between genotype-specific lignan content and plant salinity-adaptiveness, we compared two flax varieties Flanders and Astella, where Flanders has higher lignan contents than Astella. We used a 1-week NaCl stress for the study. Post-stress morphological analyses revealed comparatively higher growth arrest in Flanders, suggesting its energy and resource-saving behaviour than Astella. Salinity-mediated reactive oxygen species production and associated cell damage were relatively greater in Astella than in Flanders. In biochemical stress marker assays, we found comparatively upregulated antioxidants and osmoprotection machinery in Flanders, showing its higher ROS scavenging and cellular protection capabilities than Astella. Moreover, the two-tailed qPCR assay showed comparatively higher upregulation of three lignan biosynthesis-related miRNAs - miR168a, miR399g, and miR828a in stressed Flanders indicating its emphasised involvement of lignans in salt stress mitigation. The results depict the superiority of Flanders in salt stress mitigation over Astella.