Whether merger of two divergent genomes by hybridization at the homoploid level or coupled with WGD (allopolyploidy) can bestow plants better tolerance to stress conditions remains understudied. In this study, two diploid rice (Oryza sativa L.) subspecies, japonica, and indica, their reciprocal F1 hybrids and segmental allotetraploids were compared for phenotypic performance and gene expression under normal and nitrogen (N)-deficient conditions. We found that F1 hybrids and tetraploids showed higher tolerance at similar levels than did either parent. In parallel, total expression levels of 18 relevant functional genes were less perturbed by nitrogen deficiency in F1 hybrids and tetraploids than in the parents. This is consistent with stable intrinsic partitioning of allelic/homoeologous expression defined by parental legacy in the homoploid F1 hybrids/tetraploids between the two conditions. Our results suggest that genetic additivity at both the homoploid level or allopolyploidy may lead to similar beneficial phenotypic responses to nitrogen stress compared with their parents. The lack of synergistic responses to nitrogen limitation concomitant with WGD, relative to that exhibited by F1 hybrids, adds new empirical evidence in support of the emerging notion that hybridization by itself may play a significant role in plant adaptive evolution in times of stress.