A mapping population of recombinant inbred lines (RILs) derived from the cross between Co39 (lowland, Indica rice cultivar) and Moroberekan (upland, Japonica) was used, in two experiments to map QTLs associated with salt tolerance, particularly, ion accumulation under salinity stress by composite interval mapping (CIM). In QTL mapping study-I, plants were transplanted in compost filled pots and exposed to non saline and saline treatments (100 mol m -3 NaCl + 5 mol m -3 CaCl 2 ) in a flood bench system and data were recorded for various physiological and morphological parameters at different exposure times to salt stress. There were three replications in mapping study-I. The plants were grown only at 100 mol m -3 NaCl + 5 mol m -3 CaCl 2 salt stress in mapping study-II, with three replications. QTL mapping study-I used 32 RILs, whereas, in study-II a total of 120 RILs were evaluated for phenotypic response. The integrated genetic map of rice chromosome-1, consisting of 45 molecular markers had a distance of 201.2 cM with an average interval of 4.57 cM between markers, saturating a region that has previously been identified as a hot-spot for ion accumulation QTLs. In mapping study-II, Na + , K + concentration and K + /Na + ratio in the sap of different parts of the plant were recorded at 7 and 21 days of salt stress. A total of 38 QTLs for ion accumulation were detected in the 80 to 101 cM region of the genetic map of chromosome-1. We identified three separate regions that were active in controlling ion concentration at 21 days of salt stress, suggesting that a minimum of three different genes were acting to regulate leaf sap ion concentrations. QTLs for various physiological and morphological traits associated with salt tolerance were also detected on other chromosomes of rice. In mapping study-I, 6QTLs for Na + in expanded leaf were detected on chrom.1 (2QTLs), 2 (1QTL), 3 (1QTL) and 9 (2QTLs), whereas, 4QTLs were found on chrom.1 at 21 days salt stress in mapping study-II. Similarly, 6QTLs for K + in expanded leaf were detected on chrom.1 (1QTL), 2 (1QTL), 6 (1QTL), 7 (1QTL) and 9 (2QTLs), whereas, no QTL was identified in mapping study-II at 21 days salt stress. Regarding, K + /Na + ratio of expanded leaf 5QTLs were detected on chrom.1 (4QTLs) and 12 (1QTLs) in mapping study-I, whereas, 4QTLs were identified on chrom.1 at 21 days salt stress in mapping study-II. QTLs for these traits were also detected in other tissue types in mapping study-II. The QTLs for Na + accumulation were detected at different regions under salt stress and non stress conditions suggesting that same genes are not involved in the control of ions under salt stress and non stress conditions. Moroberekan alleles at most of the loci increase Na + and decrease K + conc. in the leaf sap under salt stress. The markers RM10710, RM8094, K061, RM3412 and RM493 are important for salt tolerance on chromosome-1 because of the presence of consistent QTLs for K + and Na + accumulation in this region. The relationship is also discussed between these QTLs and others such as Saltol, SalT, SKC-1 etc. reported by different authors. QTL for days to heading were also found under non saline conditions.