The expression of nitrate and ammonium transporter genes in the roots of winter wheat in response to drought stress is largely unknown. A greenhouse experiment was established to study the expression of five putative nitrate transporter (NRT) genes (TaNRT2.1, TaNRT2.2, TaNRT2.3, TaNRT1.1, TaNRT1.2) and three ammonium transporter (AMT) genes (TaAMT1.1, TaAMT1.2, TaAMT2.1) in the roots of winter wheat in response to soil drought under conditions of limited nitrogen (N) (no N added) and adequate N (addition of 0.3 g N kg^–1 soil). Two wheat genotypes with low and high N-uptake efficiencies were used, and water-stress treatments were applied at the vegetative and reproductive growth stages of wheat. Expression of all of the genes was quantified using real-time reverse transcription PCR. The results indicated that wheat plants growing in the N-adequate soil were more sensitive to drought stress than those growing in the N-limited soil. The response of the expression of the NRT and AMT genes to soil drought largely depends on N application, wheat genotype and growth stage. The expression of the two low-affinity NRT genes (i.e. TaNRT1.1 and TaNRT1.2) in the N-inefficient genotype XY6 was mainly induced by drought stress, but the expression of the two genes in the N-efficient genotype XY107 was repressed by drought stress. The expression of the high-affinity NRT gene TaNRT2.1 was repressed by drought stress, but the expression of the other two high-affinity NRT genes, TaNRT2.2 and TaNRT2.3, was induced or repressed by soil drought depending on N application and growth stage. The expression of the genes TaAMT1.1 and TaAMT2.1 was mainly repressed by drought stress, whereas the expression of the gene TaAMT1.2 was induced by drought stress. The expression of TaNRT2.1 in XY107 was significantly higher than in XY6.