Salt stress is currently one of the most critical factors, reducing agricultural production. Indian mustard (Brassica juncea) is a major oilseed crop in these areas. However, salt affects as much as 50–90% worldwide yield reduction. Salt tolerance is a very complex factor controlled by a number of independent and/or interdependent mechanisms and genetic modification that lead to many changes in physiology and biochemistry at the cellular level. The classical methods of plant breeding for salt tolerance involves the widespread use of inter and intraspecific variations in the available germplasm which is essential for any crop development program. This large germplasm is then tested under various salt levels in microplots, which is a quick, reliable, reproducible and inexpensive method of salt tolerance. Genotypes that have shown better indications of stress tolerance without significant yield reduction are considered to be tolerant and are also used as potential donor in the breeding programs. In this way, ICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal developed and produced five varieties of Indian mustard that tolerate high salt namely, CS 52, CS 54, CS 56, CS 58 and CS 60 in the country, and many other high-quality pipeline lines exploration and development. These salt-tolerant species work better under conditions of salt stress due to various manipulations (physiology, genes and molecular level) to fight salt stress has led to detrimental effects. Recent molecular tools to add classical breeding systems to improve saline-tolerant mustard varieties in a short span of time, including the Marker Assisted Selection (MAS) and backcrossing, that have helped using simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) markers to identify quantitative trait loci (QTLs) that control the polygenic traits like tolerance of salt and seed yield.