Submergence stress due to unpredictable soil flooding is one of the main constraints encountered in rainfed growing areas, especially in Southern Sumatran riparian swamps. The development of submergence-stress-tolerant cultivars through the introgression of Sub1 via marker-assisted backcrossing (MABC) is an ideal solution. This study was carried out during 2020 at Sriwijaya University, Palembang, Indonesia, with the aim to select Sub1-introgressed lines in BC3F1 generations on the basis of MABC and to screen out the SSR markers that were unlinked to the target gene for application in subsequent background selection studies. Results revealed that almost all the backcrossed progenies segregated from the rice parental cultivars ‘FR13A’ and ‘Pegagan’. The backcrossed lines showed significantly improved submergence stress tolerance and recovery rates compared with their parents. Sub1 introgression into the BC3F1 generation was confirmed by the tightly linked Sub1 marker SUB1C173, and marker RM23915 was used for recombinant selection. These markers followed the expected marker segregation ratio in accordance with the Mendelian single gene model. In the parental polymorphism survey, 84 out of 237 SSR markers that were unlinked to the target loci were found to be available for background study. Twenty-seven backcrossed lines were selected on the basis of foreground selection. Seven plants were selected on the basis of the recombinant marker RM23915. Five backcrossed lines were further selected on the basis of submergence stress tolerance and agronomic performance.