Drought is the major abiotic constraint leading to yield loss in rainfed areas covering 38% of total rice area. The reproductive stage is the most sensitive to water deficiency as compared to vegetative stage of rice. There are many primary as well as secondary traits for drought tolerance reported leading to linkage of multiple genes/QTLs with the traits. Still the genetic advancement in development of tolerant lines is slow and limited. Hence, in the present investigation, we aimed to study the polymorphism between two contrasting parents for drought tolerance and phenotyping for reproductive stage drought tolerance traits. A highly tolerant germplasm line CR143-2-2 and a susceptible high yielding popular variety of Andhra Pradesh state of India, Krishnahansa were used in the present study. Seventy seven markers (38.3%) distributed in all chromosomes except chromosome 4 and 5 showed polymorphism between the two genotypes. These markers were linked to 19 phenotypic traits like grain yield under drought, days to 50% flowering, harvest index, biomass, drought response index, canopy temperature, plant height, flag leaf length, leaf rolling, leaf drying, panicle exsertion, root length, 1000-seed weight, spikelet fertility, panicle weight, percentage of filled grain, seed number per panicle, root volume, root number and root penetration. The markers like RM12091, RM279, RM104, RM263 and RM523 were linked to multiple traits. The polymorphic markers obtained in the present investigation will be used to validate the developed recombinant inbred lines (RILs) and mapping of QTLs for drought tolerance.