The ultrastructure of Hypogymnia physodes (L.) Nyl. and Alectoria capillaris (Bryoria capillaris (Ach.) Brodo & D. Hawksw.) grown or transplanted near a fertilizer plant and a pulp mill was compared to normal ultrastructure of these lichen species. The ultrastructural changes observed were highly similar in the symbionts of both species and near both the factories although the emissions are different. In the lichens grown near the factories the number of algae had clearly increased. The appearance of the chloroplasts was roundish compared to controls. The pyrenoglobuli and cytoplasmic storage bodies were smaller than normally and the number of polyphosphate bodies had increased. Also, in mycobionts storage droplets were very small or absent and many vacuoles and dark inclusions appeared to hyphae in contrast to controls. In transplanted lichen there existed mainly the same ultrastructural changes as in the lichen grown near factories. Near the fertilizer plant the damage was, however, more severe because all the lichens died during 6–7 months after transplantation. Near the pulp mill part of the lichens survived and seemed to adapt to air pollution.