Abstract <p>The physiological response of the marine diatom <i>Pseudo-nitzschia pungens</i> to dark exposure for 45 and 90 days and subsequent acclimation under re-illumination was studied. We have shown that the alga remains metabolically active between day 0 and day 45 of dark exposure. This stage is characterized by the stabilization of cell culture density, activations of respiratory metabolism and synthetic processes, and a low rate of intracellular carbon (C) and nitrogen (N) consumption. Between day 45 and day 90 of dark exposure, <i>P. pungens</i> cells enter a rest state accompanied by the cessation of cell division, suppression of synthetic processes and preservation of the light-harvesting complex, and almost complete suppression of photosynthesis. The viability of cells is provided by maintaining high respiratory activity and elevated level of intracellular C reserves. We have also shown that the step-by-step reorganization of the structure and function of the photosynthetic apparatus in <i>P. pungens</i> under long-term dark conditions contributes to the maintenance of the cell’s photosynthetic competence and the subsequent recovery of the population density of <i>P. pungens</i> when re-exposed to light. The duration of the population recovery of algae, as well as the regeneration of the structure of their light-harvesting complex, is related to the length of exposure to darkness.</p>