Iron deficiency is a major constraint in rice cultivation, particularly under direct-seeded rice (DSR) systems, where aerobic soil conditions reduce iron availability in plant-accessible forms. In this study, the experiment was initiated with screening of 116 germplasm lines of two weeks old line under hydroponics iron-deficient and sufficient conditions. Based on morphological and SPAD (Soil Plant Analysis Development) values, two contrasting rice genotypes - RA23 (tolerant) and LalatMas (susceptible) were selected and investigated to determine the molecular basis of iron deficiency response through comparative transcriptome analyses. A substantial number of differentially expressed genes (DEGs) were identified in each genotype, revealing distinct transcriptional reprogramming associated with iron acquisition, transport, and homeostasis. Functional classification and enrichment analyses uncovered genotype-specific regulation of pathways related to iron ion transport, general defense and stimulus-response functions, and ADP-binding activity, indicating the involvement of signaling and regulatory proteins. A subset of candidate genes, including both known iron-responsive regulators and previously uncharacterized proteins, was further prioritized based on differential expression patterns, interaction predictions, structural features and expression profiles. Quantitative real-time PCR validation confirmed the expression patterns of selected DEGs, supporting their relevance in iron stress adaptation. Notably, the greater induction of iron transporters in LalatMas likely reflects its stronger compensatory drive to acquire iron relative to RA23. This study provides the first report of leaf-specific transcriptomic signatures associated with iron deficiency in rice and offers a valuable set of candidate genes for functional analysis and breeding of iron-efficient cultivars optimized for DSR and other nutrient-limited agroecosystems.