Salinity is a serious problem in South Bangladesh, regularly affecting about one million hectares of rice lands in coastal areas. A major QTL for salinity tolerance on chromosome 1, Saltol, provided the opportunity to apply marker-assisted back crossing to precisely introduce tolerance into popular, but salt-sensitive Bangladeshi mega-varieties. Using FL478 as a donor, the Saltol locus was introgressed into BRRI dhan28, a popular variety in the dry season, and BR11, popular for the transplant Aman season in Bangladesh. A BC3F2 homozygous individual was identified using marker-assisted selection with a 1.4 Mb Pokkali introgression at the Saltol region (10.8-12.2 Mb) with 99% recurrent parent content across the rest of the genome. Seeds of the fixed BR28-Saltol line were amplified and distributed to NARES partners for field trials. To further confirm the genome recovery, a single nucleotide polymorphism (SNP) assay was carried out where 1388 SNPs were successfully mapped in BR28-Saltol and its parental genotypes (BR28 and FL478). Four BR11-Saltol lines (BR11-Saltol-4, BR11-Saltol-5, BR11-Saltol-6 and BR11-Saltol-8) were identified in the BC2F3 generation as homozygous lines with clean background using SSR and SNP markers, and BR11-Saltol-6 was selected based on phenotypic and grain quality analysis and designated as IR89574-7. Two lines, IR89573-84 (BRRI dhan28-Saltol) and IR89574-7 (BR11-Saltol) can potentially be released as salt tolerant varieties, as they possess the same characteristics of their recurrent parents and did not show any undesirable agronomic or quality traits after introgression of Saltol locus. Furthermore, a diverse set of germplasm was characterized to identify novel sources of salt tolerance through physiological and SNP assays. Based on the overall phenotypic acceptability (SES score), plant vigor and also Na+-K+ ratio and chlorophyll content, the results confirm that Akundi, Ashfal, Capsule, Cheriviruppu, Chikirampatnai, Kalarata and Kutipatnai could be good donors for tolerance during seedling stage, and can potentially provide alternative novel sources of salt tolerance genes for breeding. Capsule, a salt tolerant, widely adapted Bangladeshi indica landrace, was used to identify new QTLs for salinity tolerance. An F2:3 mapping population was evaluated for 9 physiological and agronomic traits. A molecular linkage map was constructed using 105 simple sequence repeat (SSR) and insertion-deletion (InDel) markers. QTLs were identified on the long arm of chromosome 1 (different region from Saltol) for Na+ uptake, Na+/K+ ratio and survival; on chromosome 3 for Na+ uptake, survival and SES; and chromosome 5 for K+ uptake and SES. Thus Capsule provides an alternative source of salinity tolerance aside from Pokkali, which may be useful for future QTL pyramiding. A near-isogenic line (NIL) mapping population involving 188 BC4F2 individuals was also developed using the tolerant FL478 and sensitive IR29, to identify and map additional QTLs. An additional large effect but novel QTL was identified on the long arm of chromosome 1, (different region than Saltol and SKC1) for Na+ concentration (qNa1.2) and Na+-K+ ratio (qNaKR1.1). In addition, a cluster of large effect QTLs was identified on chromosome 12 for Na+ concentration (qNa12.5) and Na+-K+ ratio (qNaKR12.3) and QTLs with relatively large effects were identified on chromosome 3, 5 and 10, which are also considered novel. These additional loci can subsequently be used for QTL pyramiding, together with Saltol locus, to obtain a level of tolerance similar or even higher than that conferred by FL478. Thus, the QTLs identified on chromosomes 1, 3, 5, 10 and 12 that are associated with salinity tolerance at seedling stage remain good targets for QTL fine-mapping and subsequent pyramiding to develop highly tolerant varieties. The allelic diversity of 107 cultivated rice germplasm has been characterized using molecular markers (RM1287, AP3206f, RM3412b, RM493 and RM7075) linked to Saltol locus and a high-throughput 384-plex SNP platform. The polymorphism information content (PIC) values ranged from 0.15 (AP3206f) to 0.80 (RM3412b), with an average of 0.55 for the SSRs and averaged 0.35 across the SNP markers. One cluster was identified as aus with the tolerant landrace Kalarata falling within that cluster. All the Pokkali accessions were grouped into a different sub-cluster and considerable variation was observed among the Pokkali accessions. Finally, the promising novel donors identified in this study, Akundi, Ashfal, Capsule, Cheriviruppu, Chikirampatnai, Kalarata and Kutipatnai are genetically different from Pokkali and Nona Bokra, confirming their potential as novel sources for salinity tolerance.