Submergence is one of the important abiotic stresses incurring substantial loss to rice production in Bangladesh. With a view to improving submergence tolerance in BR22 (popular name Kiron) is a promising antioxidant enriched, high yielding and strongly photosensitive transplanted Aman rice variety, BRRI dhan 51 was used as a donor parent to introgress the SUB1 QTL conferring submergence tolerance. Molecular marker within submergence tolerant QTL (SUB1), flanking markers and evenly distributed background markers were utilized in a marker aided selection program to develop advanced breeding lines with broad-spectrum tolerance to flash flooding submergence. Indel and simple sequence repeats (SSRs) markers were used in the marker assisted backcrossing scheme in BC4F1and BC5F1 generation. Sub1C173 a gene specific indel marker SUB1 QTL was used to select plants possessing the tolerant genes (foreground selection). The result of recombinant selection also revealed that the size of the SUB1 QTL introgression from the donor parent was estimated as 2.5 Mb. The percentage of recipient genome recovery in the best plant viz. BR10190-3-1-20-3 was 95%. This research work illustrates the successful application of marker-assisted breeding to introgress the submergence tolerant QTLs into the genetic background of BR22.