The effect of UV and visible light on cyanobacteria was determined at the cellular level by means of epifluorescence and confocal microscopy techniques. These methods allow the examination of light effects in spatial resolution. Series of measurements were performed to determine the effect of different light qualities and quantities on cyanobacteria. To analyze the effect of the light quality, samples of Anabaena and Scytonema sp. were exposed to intense blue, green or red light applied from the epifluorescence path of the microscope. The fluorescence of the phycobiliproteins was recorded by means of epifluorescence (excitation 550 nm, 20 nm half band width (HBW), emission above 635 nm) or by confocal microscopy (560 nm laser line). Upon exposure to blue or green light the cells showed an increase in fluorescence followed by a sudden and complete loss of fluorescence. Blue light was more effective (bleaching of phycobiliproteins within 45 min) than green light (bleaching within 120 min). Red light was not as effective, and bleaching of the cells took at least 24 h. Initially the cells showed an increase in fluorescence followed by fast bleaching of the fluorescence signal. Cells exposed to UV plus PAR were bleached within 60 min, while cells exposed to photosynthetically active radiation (PAR) only were totally bleached after about 120 min. FL-DHP (dihydropyridine) labeling was performed in two cyanobacteria, Anabaena sp. and Nostoc commune, to visualize L-type calcium channels. Both cyanobacterial strains showed a pronounced FL-DHP signal of the heterocysts and akinetes but only a weak signal from the vegetative cells. The results clearly indicate the presence of calcium channels in these cells. UV radiation decreased the amount of chlorophyll and phycocyanin as could be seen from a decline in the autofluorescence of the cells. In contrast, the FL-DHP signal was not affected by UV.