Drought stress is usually preceded by moisture stress conditions that triggers the plant to acclimate and adapt for the upcoming stress conditions. In the present study, two contrasting genotypes, ICC 4958 (drought-resistant) and CSJ 513 (drought-sensitive), were lysimetrically screened under normal and moisture-stressed conditions at the flower initiation stage. The study recorded various phenological, morpho-physiological and anatomical attributes to analyse any damage under reduced moisture conditions. The genotype ICC 4958 exhibited early flowering to avoid stress and expanded its root surface area by 2.7 times during the flower initiation stage under moisture stress conditions. However, both genotypes recorded cellular damage i.e. membrane permeability index (51.07%) and decreased leaf viability (34.70%) under mositure stress, with CSJ 513 being more affected than ICC 4958. Root analysis via SEM evidenced thickening of parenchyma and increased metaxylem vessels in the root of ICC 4958. Semi-quantitative PCR amplification studies found an expression of a specific gene, LEA6, in ICC 4958. A phylogenetic study using the homologous sequences reveals the distinctness of the two genes from the other family members. We detected five and two highly conserved regions in LEA3 and LEA6 genes respectively, through multiple sequence alignment, which might play a role in biotic stress tolerance.