A study was conducted at Main Agriculture Research Station, Raichur with an objective to observe the morpho-physiological changes of rice under direct seeded (DSR) and transplanted rice cultivation (TPR). Significant difference was observed among the three genotypes and three graded level of fertilizer (75% RDN, 100%RDN and 125% RDN) in both the water management system. Higher plant height, number of green leaves, tiller count, leaf area was observed in TPR compared to DSR. Genotype JKPH 3333 record significantly higher dry matter production 13.6 g/ hill-1 under 125% RDN during reproductive phase in TPR as compared to DSR. Greater dry matter accumulation resulted in higher yield production (60.98 q ha-1) in JKPH 3333 with 125% RDN followed by genotype Gangavathi sona(55.45 q ha-1) and BPT 5204 (52.44 q ha-1). The indicated that infrastructure of plant is decided by morphological parameters coupled with more photosynthetic activity which lead to higher biomass production and also efficient partitioning of dry matter in to reproductive parts. It was understood that variety including nitrogen levels and its suitability to each method of cultivation and varieties differing growth habit and duration behave differently under different situations. Detailed investigation on characterization of varieties to different management practices help farmers to upheld there farm income and effective nutrient management in rice cultivation.