Drought is one of the serious abiotic stresses limiting rice productivity under prolonged dry spells. The present study was aimed to estimate heritability of yield and its components under lowland stress for direct selection of yield in fifty advanced back crosslines derived from drought susceptible Samba Mahsuri and tolerant Azucena besides screening with yield QTL linked molecular markers. High heritability for broad sense was observed in days to 50% flowering followed by spikelet fertility and grain yield plant^-1 indicating direct selection for yield under stress is practicable in evolving drought tolerant rice varieties with yield potential. Thirty one advanced back cross lines (BC2F3) lines co segregating for simple sequence repeats (SSRs) linked to yield QTLs under low land stress viz., RM 520 linked to DTY 3.1 on chromosome 3 and RM 236 linked to DTY 2.1 on chromosome 2 exceeding yield of susceptible parent were advanced to BC2F4. These results suggested that direct selection for yield under water stress coupled with marker assisted screening would help in precise selection of genotypes for drought prone areas.