Two hundred fifty three BC2F2 rice lines of the OM7347/OM5629 were evaluated at seedling stage in the green house of CLRRI. Molecular markers associated with salt tolerance QTLs were identified by using 416 polymorphic SSR markers. QTLs associated with stress tolerance at EC = 8 dS/m at seedling stage, detected from the BC2F2 population, were located on chromosomes 1 and 3. Three QTLs were identified within the intervals of RM3532-RM10694, RM3740-RM5336, and RM11125-RM9 at map positions of 4.4, 4.5, and 18 cM on chromosome 1, respectively. Two QTLs were located within the intervals of RM3867-RM6959 and RM6876-RM4425 at map positions of 4.5 and 18.0 cM on chromosome 3. Three QTLs in the regions of RM1324-RM2412, RM1185-RM24, and RM1282-RM2560 on chromosome 1, and one QTL of RM453-RM511 on chromosome 12, were associated with salt tolerance at reproductive stage (EC = 4 dS/m). In addition, three advanced backcross populations were developed as BC2F2 of OM6162/Pokkali (100 lines), BC3F2 of OMCS2000/Pokkali (50 lines), BC3F2 population of OM1490/Pokkali (53 lines). Their phenotypes were evaluated at seedling and reproductive stages. Marker-assisted selection was applied to identify promising lines using the markers RM3252 and RM223.