Regulation of root system growth and architecture is an adaptive mechanism evolved by plants to cope with variable nitrogen availability in the soil. In grafted plants, this process depends on intrinsic properties of the rootstock as well as long-distance signaling between each partner of the graft (scion and rootstock) and contributes to the fitness of the whole plant. We show here that two grapevine rootstock genotypes known to differentially control scion growth have developed two distinct root development strategies to optimize nutrient uptake in response to nitrogen availability. The rootstock '1103 Paulsen' conferring high vigor developed a deeper root system and a larger number of lateral roots than 'Riparia Gloire de Montpellier' (RGM), a rootstock that confers low vigor, whatever the nitrogen concentration in the culture medium. RGM cuttings grew surface roots and developed lateral roots only with low nitrogen supply. This developmental pattern suggests that RGM promotes lateral root production when nitrogen content is limiting to increase its prospecting area for the uptake of nitrogen resources. Gene expression profiling revealed interesting patterns and differences between the two studied rootstocks, particularly concerning hormone signaling.