Lichens are classified as extremophilic organisms due to their high resistance to abiotic stresses, including UV radiation and heavy metals. Among the protective mechanisms of lichens to adverse environments, secondary metabolites, including melanins, play a special role. The foliose cyanolichen Lobaria retigera responds to high solar radiation by synthesizing dark brown melanic pigments in the upper cortex. However, the morphological and physiological traits of melanized thalli of L. retigera are unknown. In this study, we examined the microstructure of pale and naturally melanized thalli of the lichen L. retigera. We also studied the protective effects of melanin on the tolerance of L. retigera to high light and heavy metal stress. Here, for the first time we used immunolabeling to confirm that the melanic pigment in the hyphal lumens of the upper cortex of L. retigera is eumelanin. Melanized thalli displayed thickening of the cell walls, and we detected deposits of metabolites in the hyphal lumens, including spherical melanin-like granules. Atomic force microscopy was applied to study the nanomechanical characteristics of cross sections of the upper cortex. Results showed that in melanized thalli the adhesion values were reduced to almost half compared to those of the pale thalli. Furthermore, measurements of PSII activity and ion leakage showed that melanized thalli of L. retigera displayed significantly greater tolerance to photoinhibition and toxicity of the heavy metal Cu. It seems likely that the physicochemical properties of melanin from L. retigera are responsible for its protective effects. Consistent with this, extracted melanin absorbed strongly in the UV region and displayed high paramagnetic properties. Taken together, results from this study indicate that anatomical changes in the upper cortex caused by melanization and also the physicochemical properties of the melanin facilitate the higher tolerance of L. retigera to excess light and heavy metals. Keywords: Lichens; Melanin; Antibody; Ultrastructure; Heavy metal.