Aerobic adaptation could be an important modification in the traditional rice to cope up with the increasing water scarcity problem. Identification of stable QTL for traits promoting adaptation to aerobic conditions can facilitate the development of water-efficient aerobic rice varieties with better yields. Filial and backcross populations derived from the crosses between high-yielding low-land (HKR47) and aerobic (MAS26) indica rice varieties, were evaluated for various physio-morphological traits including root traits (in case of net house evaluation). Under aerobic field conditions, grain yield per plant showed significant positive correlation with plant height, effective number of tillers/plant and panicle length in all the populations. Grain yield per plant also showed positive correlation with root length in both filial populations and with fresh and dry root weight in F2 population. Two parental rice varieties displayed polymorphism at 125 of the 803 SSR loci, which were used to map the QTL associated with traits promoting aerobic adaptation. A total of 14 QTL were detected, 10 of them were identified on chromosome 8. Study led to the identification of a number of promising plants with higher grain yield, better root length/biomass under managed aerobic conditions and possessing most of the identified QTL.