The benefits of developing and releasing salinity-tolerant and phosphorous-deficiency-tolerant rice in Bangladesh, India, Indonesia and the Philippines were estimated for marker-assisted breeding as compared to conventional breeding using economic surplus analysis. Marker-assisted breeding is estimated to save at least 2 to 3 years in the breeding cycle and result in incremental benefits over 25 years in the range of $300 to $800 million depending on the country, stress, and time lags. Salinity and phosphorous deficient soils are difficult problems to solve through conventional breeding because of “genetic load” or undesirable traits that accompany desirable ones during backcrossing. MAB, enabled by advances in genomics and molecular mapping is more precise and hence time-saving. Solving salinity and P-deficiency problems is important, regardless of whether MAB or CB is used, as the cumulative benefits are at least $220 million and as much as $4 billion over the next 25 years depending on the problem and country.