Thirty days old rice seedlings of 300 F5:6 recombinant inbred lines (RILs) derived from a cross between a salt sensitive, IR29 (indica), and a salt tolerant, Hasawi (indica), were evaluated for salinity tolerance and thereafter QTLs linked to salinity tolerance were identified. Large variation in salinity tolerance among the RILs was detected. Final salinity injury scores ranged from highly tolerant to highly sensitive with a transgressive segregation towards sensitive parent. However, for the other studied parameters, RILs showed transgressive segregation on both parental sides. One hundred ninety four polymorphic SNP markers were used to construct a genetic linkage map involving 142 sorted RILs based on final salt injury scores. The SNPs covered 1441.96 cM genome with an average distance of 7.88 cM between loci. Twenty QTLs (LOD>3)were identified on chromosome 1, 2, 4, 6, 8, 9, and 12 using composite interval mapping for eight studied traits in salinized (EC 12 dSm-1) Yoshida nutrient culture solution following IRRI standard protocol. Two QTLs were located on chromosome 1; three QTLs on chromosome 2; three QTLs on chromosome 4; three QTLs on chromosome 6; one QTL on chromosome 8, two on chromosome 9, and six QTLs on chromosome 12. The QTLs identified on chromosome 1 (qSL1.1) were located on long arm of the chromosome 1, which is a very different position from Saltol locus. This was the major QTL explaining 20.6% of the total phenotypic variation for shoot length. Five out of six QTLs identified on chromosome 12 were located at 6.9 cM position. Fine mapping of these novel QTLs in a different genetic background is suggested. Novel QTLs could be useful to enhance the level of tolerance through MAS for the pyramiding of different QTLs in one background.The International Rice Research Institute (IRRI)