Salinity stress is one of the major abiotic stresses affecting rice (Oryza sativa L.) production, as rice is the most susceptible cereal crop to salt stress. A population of 174 F10 – F12 recombinant inbred lines derived from an IR64 (indica) x Azucena (japonica) cross was evaluated under control and salt stress conditions at pre-emergence seedling stage using a novel phenotypic platform. The phenotypic results indicated that the abscisic acid and sugar content in shoot meristem region increased due to salt stress whereas the growth related traits were negatively affected. The mapping study successfully identified 27 QTLs under control conditions and 25 QTLs under salt stress conditions for shoot meristem weight, shoot meristem glucose, sucrose and total sugar content, shoot length, primary root length, lateral root count and length traits with LOD scores ranging from 3.7 to 9.9. Many of the QTL locations matched with previous studies and some novel QTLs were also identified in this study.