Water availability is one of the major limiting factors that seriously influence rice production in the rainfed ecosystems and rice genotypes exhibit differential response to drought stress. With an objective to understand the physiological factors and the genomic loci that influence the tolerance to drought stress in rice, five weeks old seedlings of 38 rice genotypes were subjected to drought stress for 5, 7 and 9 days. Significant variation was observed for traits like shoot length, root length and tiller number plant-1 in all the treatments studied and 14 genotypes displayed higher levels of tolerance similar to controls. Among the physiological traits, high relative water content (> 75%) under severe drought stress, was recorded in 10 genotypes while 10 genotypes recorded higher levels of proline accumulation under stress. Eight genotypes and CR-143-2-2 (control) possessed high levels of tolerance to drought stress. In the molecular analysis with thirty microsatellite (SSR) markers linked to different drought tolerance QTLs, twelve markers confirmed the association of the markers with the associated drought tolerance traits in these tolerant genotypes.