Under the present study, assessment of genetic variability of 60 numbers of rice landraces was carried out under morphological and molecular level for selection of promising drought tolerant genotypes under upland ecosystem of North East India. Predominance of additive gene action on characters like leaf rolling index, root: culm ratio, grain yield and other yield contributing traits like plant height came out as effective parameters for selection of drought stress tolerant landraces.  Molecular analysis revealed moderate genetic diversity with average Polymorphic Information Content values of 0.44 across the rice landraces. No specific clustering patterns of landraces against some morphological traits numbers of productive tillers per plant, numbers of filled grains per plant etc were found. This signifies the polygenic nature of the quantitative characters and influence of environment on them. Precise correlation between the morphological performance of the landraces and their clustering pattern under molecular analysis was found to be effective in identifying suitable landraces like Chikanswarikabar as a promising parent for future breeding programme and also to formulate efficient strategies for sustainable management of rice landraces under rain fed ecosystem.