Tolerance to ammonium nutrition in plants can be related to their ability to detoxify ammonium via nitrogen assimilation in roots. Here, we report that sorghum–sudangrass (Sorghum bicolor L. × S. bicolor var. sudanense) hybrids exhibited enhanced biomass production under high levels of inorganic nitrogen supply as well as increased capacity for nitrogen assimilation in roots. Glutamine synthetase (GS, EC 6.3.1.2) activity and protein accumulated in roots at increasing concentrations of either nitrate or ammonium, with particularly high levels of GS in ammonium-treated plants. Ammonium but not nitrate differentially regulated two distinct cytosolic GS (GS1) isoforms composed by polypeptides of similar size but different charge. The comparative analysis of GS gene sequences and the deduced GS1 polypeptides suggested that the two GS1 isoforms were the expression products of SbGln1.2 and SbGln1.3 genes. SbGln1.3 expression was shown to be upregulated by high levels of inorganic nitrogen supply, with a maximal abundance of SbGln1.3 transcripts in ammonium-grown plants. SbGln1.2 expression was uniform along the root axis meanwhile protein and transcript levels for SbGln1.3 were particularly abundant in the upper part of the axis where lateral roots are prominent. Kinetic analysis revealed that the two GS1 isoenzymes have relatively low-affinity for ammonium ions. The spatial distribution of low-affinity GS1 isoenzymes would provide a sustained glutamine biosynthesis at high levels of ammonium supply and may represent at the same time an efficient system of ammonium detoxification. Such a mechanism may prevent transport of ammonium to leaves alleviating symptoms of toxicity and therefore contributing to sorghum ammonium tolerance.