The photobiont ultrastructure of the epiphytic lichens Bryoria fuscescens and Bryoria fremontii was studied along the pollution gradient from two Cu-Ni smelters in Nikel and Monchegorsk in northern Finland and north-western Russia. The relationship between ultrastructural characteristics of B. fuscescens and environmental factors (i.e. climate, atmospheric SO2 and bark element concentrations) was studied by using a principal component analysis (PCA) aiming to assess the air quality in a northern environment. Based on PCA, increased plasmolysis and mitochondrial changes in the Trebouxia photobiont were significantly correlated with elevated pollutant concentrations. Degenerated cells, showing altered chloroplasts and electron-translucent pyrenoglobuli, occurred in lichens growing 35–50 km from the Monchegorsk smelter. Cell wall and cytoplasmic lipid volumes, and size of pyrenoglobuli, positively correlated with the distance from the Monchegorsk smelter. Vacuoles and electron-opaque vacuolar deposits were significantly increased at the Finnish site in the vicinity of a pulp mill. Swelling of mitochondrial cristae and thylakoids showed little correlation with environmental factors, but indicated of initial stage of injuries and were observed at several slightly polluted sites in northern Finland and north-western Russia. The results suggest that the severe photobiont injuries of lichens are strongly associated with poor air quality.