Abstract Heavy metal and dust pollution absorption through lichen thallus occurs on the surface, that is by means of ectohydric sorption . Protective mechanisms, among which there is heterometric (layered) structure of lichens, play a significant role in limiting this process. The aim of this research was to determine the way the pollution penetrates inside lichen thallus and to determine the role of dermal layer in stopping heavy metals on the thallus surface . Lichen thalli exposed to transport pollution near Krakow-Katowice motorway for half a year were analyzed. With the use of Electron Scanning Microscope Quanta 250 and microanalyser EDEX accumulation of pollutions depositing on the outer lichen surface, on the surface of algal cells, in subcortex layer, on the fungal hyphae surface and intercellular spaces of crack bottom of pseudocyphella were determined. The results of the analysis show an important role of pseudocyphella in the process of pollution penetration inside lichen thallus and protective effectiveness of the upper cortex whose tight structure and thickness of chitinous cell walls of mycelium, relatively thicker in comparison to parenchyma layer, influence its dermal properties. Heavy metal accumulation (Al, Fe, Cu) on the thallus surface, on algal cell surface, on the fungal hyphae surface and deep layers of pseudocyphella cracks is presented by the order: crack > alga > fungi > subcortex layer > thallus surface.