Due to negative effects of the unused Nitrogenous fertiliser on the environment and high cost of production associated with N fertilisers, improvement of Nitrogen use efficiency in wheat has become an important breeding objective. The present research was carried out during Rabi 2019-20 and Rabi 2020-21 to evaluate the comparative response of Triticum aestivum, Triticum durum and Triticum dicoccum for NUE and related traits at two N levels (moderate N: N50 (50 kg ha-1) and control N: N100 (100 kg ha-1)). The evaluation of genotypes showed that sufficient genetic variability was found to exist within and among the three species for N use efficiency and related traits. Grain yield/ha, harvest index and above ground biomass/ha were identified as important traits for improvement of N use efficiency in a genotype via their contribution to NUpE and NUtE. Triticum aestivum genotypes showed higher N use efficiency followed by Triticum dicoccum and Triticum durum. The best performing genotypes in Triticum aestivum, Triticum durum and Triticum dicoccum were GW 322 (24.35 kg kg-1), MLT DW RI 8 (14.59 kg kg-1) and NP 200 (18.99 kg kg-1) respectively. GW-322 performed better than the checks whereas the best performing genotypes in durum and dicoccum wheat could not outperform the checks. Principal component analysis also delineated importance of the identified traits and differential response of the three wheat species for those traits. A root phenotyping study was also carried out using the same set of genotypes in soil columns at N50 and N100 to compare root traits and N uptake of the wheat genotypes across three depth zones (0-30 cm, 30-60 cm and > 60 cm. The data was collected using image-based phenotyping and analysis. Root length density was found to be an important trait whose variation at different depths of the soil governs the N uptake efficiency of a genotype. Root length and related traits recorded higher mean value at N50 and a greater variance was observed for most root traits at N100. The effect of N level was significant for all the N uptake traits including above ground biomass (AGB), N (%), above ground N (AGN) and Nitrogen uptake efficiency (NUpE). For N uptake efficiency, only the genotype effect was significant. The response of a species for a trait was dependent on the N level as well as the rooting depth. Among aestivum lines, WH1022, UASBW-13354 and RAJ 4248 performed better in terms of N uptake efficiency. MLT DW RI 8, UAS 446 and ECI26374 among durum wheat genotypes and DDK50421, NP200 and DDK50332 among dicoccum genotypes were found to have superior performance for NUpE. The current study delineates the importance of evaluation of roots at different depths instead of whole root systems and use of competitive N levels in NUE research so that the N use efficient varieties can perform equally well in the field at moderate N levels. The findings of this study can be used for recommendation of genotypes for low input environments.