Reactive oxygen intermediates (ROIs) and reactive nitrogen intermediates (RNIs) have now become well established as important signalling molecules in physiological settings within microorganisms, mammals and plants. These intermediates are routinely synthesised in a highly controlled and transient fashion by NADPH-dependent enzymes, which constitute key regulators of redox signalling. Mild oxidants such as hydrogen peroxide (H2O2) and especially nitric oxide (NO) signal through chemical reactions with specific atoms of target proteins that result in covalent protein modifications. Specifically, highly reactive cysteine (Cys) residues of low pKa are a major site of action for these intermediates. The oxidation of target Cys residues can result in a number of distinct redox-based, post-translational modifications including S-nitrosylation, S-glutathionylation; and sulphenic acid, sulphinic acid and disulphide formation. Importantly, such modifications precisely regulate protein structure and function. Cys-based redox switches are now increasingly being found to underpin many different signalling systems and regulate physiological outputs across kingdoms.