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•The study presented an approach to understand physiological and morphological adaptive responses of Oryza sativaL. to hexavalent chromium (Cr6+) stress.•Lalat upland is more sensitive to chromium toxicity than Swarnaprabha at higher chromium concentrations.•Higher chromium concentrations reduced various physiological traits, photosynthetic pigments content in both the genotypes, and this decline was more pronounced in Lalat upland.•Variation in glandular and non-glandular trichome density and length was found in the leaves of chromium stressed plants in both the genotypes.•Stomatal guard cell deformation and closed stomatal aperture was visualised in 100 µM dichromate treated Lalat upland genotype. Abscisic acid and Salicylic acid content and expression of NCED1 and NCED2 genes involved in stomata aperture regulation.