Melatonin is known to improve the tolerance of plants to adverse abiotic factors (AAF), including dehydration. Nevertheless, details of the action of this phytohormone are not sufficiently comprehended. In the current study, the effects of melatonin on the growth, water status, and content of malonic dialdehyde were evaluated in etiolated seedlings of narrow-leaved lupine (Lupinus angustifolius L.) subjected to dehydration. The respiration of mitochondria isolated from different organs of these plants was also analyzed. Here, the 4-day-old seedlings have been deprived of water for 1 day. This entailed the increased water deficit up to 22% in the roots and 6% in the hypocotyls. Such desiccation of the seedlings retarded the growth of their hypocotyls but increased that of the roots by 13% in comparison with the undesiccated control. Both root and hypocotyl tissues accumulated MDA under these conditions. The dehydration of the seedlings negatively affected the respiration of the mitochondria isolated from these organs. The rate of oxidation of the substrates, especially malate, was diminished at the metabolic State 3 mainly due to an inhibition of the cytochrome respiration pathway (CP). For example, upon oxidation of malate, the activity of CP decreased 1.8 times in the mitochondria from hypocotyls and four to five times in those from roots. Pretreatment of the seedlings with 0.1 µM melatonin prevented the dehydration-induced rise in the MDA level in the hypocotyls but, by contrast, stimulated this parameter by 27% in the roots. Under drought conditions combined with exogenous melatonin, the growth of hypocotyls was close to that in the undesiccated control, while the root growth was lower than that in the control. In the seedlings normally supplied with water, treatment with melatonin did not significantly influence the respiration of the mitochondria prepared from the hypocotyls or roots. However, under water shortage, melatonin completely blocked the inhibition of a substrate oxidation in the hypocotyl mitochondria, chiefly because of sustaining the CP activity. As a result, exogenous melatonin increased the rate of malate oxidation by 87% and succinate oxidation by 26% in metabolic state 3 in the mitochondria from the hypocotyls. Application of this hormone to the plants only partially reversed the dehydration-induced inhibition of the oxidative phosphorilation in the root mitochondria. In this case, the oxidation of respiratory substrates, especially succinate, and activity of CP were still inhibited. Possible causes of the differences between the hypocotyl and root cells of the lupine seedling in their responses to melatonin and water deficit, namely, an extent of oxidative stress and functions of mitochondria, are discussed.