<p>Rice (<i>Oryza sativa</i> L.) is a staple crop of immense global significance whose productivity is increasingly jeopardized by various environmental stresses exacerbated by the ongoing impacts of climate change. Soil salinization is one of the most detrimental stress factors that impairs nearly all growth and developmental stages of the crop. It disrupts the key physiological processes that ultimately lead to reduced growth, yield, and quality. Rising seawater levels and salt intrusion into cultivable lands are worsening the scenario. Previous studies have mostly focused on salt-tolerance at the seedling stage under controlled conditions, which may not always be sustained at later reproductive growth stages. Additionally, the impact of saline stress on the major grain micronutrient contents, which are crucial for human nutrition, remains unexplored. This study aimed to identify salt-tolerant rice genotypes from a diverse panel of 118 landraces that could retain grain zinc and iron levels under natural saline conditions. Results revealed distinct morphometric trait associations under varying growing conditions and identified Na⁺/K⁺ ratio, days to 50% flowering, productive tillers per plant, unfilled grains per panicle and fertility percentage as critical traits influencing genotype performance under salinity stress. The dual-level screening further included 29 salt-linked microsatellite markers. Marker RM10740 exhibited the highest PIC value, and marker OsCAX(T) showed the highest number of alleles. Based on phenotypic and molecular screening, landraces Bhutmuri, Okhrajhama, Madhabi, Machkantha, Talmugur, Naichi, Kuthir and Tapan 2 were identified as true salt-tolerant accessions. These landraces can be used as novel alternative sources for further breeding programmes to enhance salt tolerance and to understand the tolerance mechanism in rice.</p>