Abiotic stresses such as salinity and phosphorous (P) deficiency are major yield-limiting factors for rice, particularly on marginal lands. Marker-aided backcrossing (MAB), enabled by advances in genomics and molecular mapping in recent years, is said to be a more precise, time-saving, and cost-effective way to develop rice varieties that can withstand these abiotic stresses than conventional breeding. The study employs the economic surplus approach to measure the benefits of MAB for salinity tolerance in rice for Bangladesh, India, Indonesia, and Philippines, and for rice with tolerance to P-deficient soils in Indonesia. At a 5% discount rate, the benefits over 15 years of planting salt-tolerant varieties amount to $226.9 million in the Philippines, $3.666 billion in Bangladesh, $4.848 billion in India, and $895.7 million in Indonesia. The gains from growing varieties that can withstand P deficient soils in Indonesia amount to $2.070 billion. The incremental benefits from completing the salt-tolerant and P-deficient tolerant breeding cycles 2 years earlier are $340.5 million in Bangladesh and $192.1 in Indonesia, respectively. In India, $227.0 million is gained even if MAB develops salt-tolerant varieties just a year earlier. The additional gains from completing the salt-tolerant rice breeding cycle 4 years earlier are $40.3 million in the Philippines and $158.9 in Indonesia. In general, the gains from saline- (Bangladesh, Indonesia, Philippines) and P-deficient (Indonesia) tolerant rice are reduced by 5%, 9%, 14%, and 18% when MAB breeding cycle is delayed by one, two, three, and four years, respectively. In India, there is 3%, 7%, 10%, and 13% loss in benefits from salt-tolerant rice for every additional year of delay in the MAB breeding cycle.