Reactive oxygen/nitrogen species (ROS/RNS) are potentially cytotoxic molecules because they can generate oxidative/nitrosative stress. However, ROS and RNS, at concentrations tightly regulated by antioxidants, serve also useful purposes in processes such as organ development, abiotic and biotic stress response and redox signaling. Antioxidant enzymes and metabolites are abundant in plants and particularly in legume nodules. Most of the enzymes involved in antioxidant defense are encoded by multigene families and occur as multiple isoforms in various cellular compartments, forming a dynamic network that is spatio-temporally regulated. Genomic, transcriptomic and proteomic analyses of model legumes, such as Lotus japonicus and Medicago truncatula, are unveiling a complex regulation of antioxidant pathways in different tissues and especially during the symbiotic interaction with rhizobia. This regulation includes alternatively spliced forms of the genes and post-translational modifications of the proteins, which with no doubt will be the subject of intense research over the next years.