This study is devoted to the ecomorphology and ultrastructure of cyanophytes on limestone rocks collected in the Szopczański Gorge (Pieniny Mountains) during the years 2006-2008. There were selected cyanophyte species for examination such as following: Nostoc microscopicum, Phormidium favosum, Leptolyngbya foveolarum, Tolypothrix distorta var. penicillatum, Pseudanabaena catenata. The ultrastructural analysis (TEM) confirmed that the structure and placement of the thylakoids is genus/species specific.