Nitrate reductase (NR) is the key rate-limiting enzyme of the nitrogen (N) assimilation process in plants, which has not been characterized in bread wheat under nitrogen stress, especially with respect to their homeologues. Total 9 NRs were identified and classified into three groups, which showed a close relationship with different wheat ancestors. The occurrence of N-responsive cis-acting regulatory elements like MYB, MYC, G-Box, and GATA-motif confirmed their N-responsiveness. Expression of all three groups of NR under N-stress revealed the NR 6-1ABD group to be the most N-responsive, which was characterized further in detail. The study was carried out in two genotypes contrasting for their N-responsiveness (HD 2967: Highly responsive to applied N, and Choti Lerma: Less responsive to applied N) selected on the basis of field evaluation. Homeologous differences within a genotype were found much more than the genotypic differences of a specific homeologue coding sequence. Among the three homeologues, though NR 6-1D homeologue was found to be most responsive to N-stress, the contribution was maximum for this homeologue, followed by NR 6-1A and least by NR 6-1B. We found that the expression of homeologues was linked to the presence of N-responsive cis-elements. All the homeologues of NR 6-1 in Choti Lerma were found less responsive to N-stress in comparison to HD 2967, which might also be linked to N-use efficiency. Homeologous expression of NR 6-1ABD revealed the negligible contribution of B-homeologue to N-stress. Homeologous differences of NR 6-1ABD was found much more than the genotypic differences. Hence, our study on wheat NR will be helpful in manipulating the specific homeologue of the NR gene in the future.