This study focus on developing new salinity tolerance and high yielding rice lines, using markers assisted backrossing (MABC) as a high technology tool for breeding. Total of 500 SSR markers on 12 rice chromosomes were screened for parental polymorphic markers. Of which, 52 primers in the Saltol region were checked with the two parents varieties to identify polymorphic primers for screening the Saltol region of the breeding populations. An analysis of 63 SSR markers on approx. 500 plants for each backcross generation of ASS996/FL478 for three steps selection. The two BC1F1 plants P284 and P307 which had the highest recipient alleles up to 89.06 percent and 86.36 percent, were chosen for the next backcrossing. Three BC2F1 plants with the recipient alleles up to 94.03 and 93.18 percent were used to develop BC3F1 generation. The best BC2F1 plant was P284-112-209 with all the recipient alleles and Saltol region. The four plants P307-305- 21, P284-112-195, P284-112-198, P284-112-213 were the second ranking with only one loci heterozygous (applied 63 markers covered on 12 chromosomes). These five plants were chosen as the breeding lines for result of Saltol.AS996 introgression. The breeding line BC4F1 having 100 percent genetic background of donor variety is ready for develop new salinity tolerant variety ASS996-Saltol to cope with climate change.