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The habitat of lichens spreads from the shores of the Arctic Ocean to the Antarctica, which is mostly explained by their highly adaptive capabilities to extreme environments. The fast restoration of the metabolism after the dehydration of the thallus is one of these capabilities. As long as photosystem II is one of the main targets of desiccation-induced damage, the defense strategy of lichens includes the minimization of the amount of solar radiation reaching PS II to maximize their endurance while desiccated and their recovery upon rehydration process. The state of the photosynthetic apparatus can be studied with time-integrated and time-resolved fluorescence spectroscopy, which is especially suitable for monitoring the influence of the environment on the Chl molecules in PS II. Photoprotective mechanisms were studied on the tripartite lichen Peltigera aphthosa that exhibits external cephalodia, collected on Kindo peninsula, Karelia, near the White Sea Biological Station of Lomonosov Moscow State University. Using the methods of steady-state and time-resolved fluorescent microscopy and Fluorescence Life-time Imaging (FLIM), we studied the dynamics of the rehydration process in different parts of the lichen thalli. It was found that apical, medial and basal parts of the thallus are not only morphologically different, but also show completely different morphological characteristics of the photobiont. In the dry state, the main contribution to the fluorescence spectrum of lichen is emitted as green fluorescence of hyphae forming the upper crust, which is rapidly and almost completely quenched during the rehydration process. Probably this is one of the protective mechanisms that reduce the amount of light reaching the PS II reaction centers in the dry state. In the process of rehydration, we observed an increase in the intensity of the chlorophyll fluorescence of the photobiont at 680 nm, with significant changes of the fluorescence lifetimes and the ratios of fast and slow components that contribute to the fluorescence decay kinetics. While in dry state, the Chl fluorescence is strongly quenched (opposite to the fluorescence of the hyphae), and the time constants recover to the typical decay times of active photosynthetic organisms during rehydration. The quantitative behaviour of these changes differed largely between the apical, medial and basal parts of the thallus, probably due to the complex interactions of the fungus, algae and cyanobacteria.