**Abstract**

Self-fluorescence of light-harvesting complex is a powerful tool for investigation of living photosynthetic microorganisms. As the physiological state of single cells of such microorganisms is closely related to the operation and activity of photosynthetic system, any variations in spectroscopic properties of their self-fluorescence indicate the changes in their physiological state. In this chapter, we present several applications of confocal laser scanning microscopy (CLSM) for investigation of living photosynthetic cells. A set of ordinary CLSM techniques will be applied for studying of cyanobacteria (or blue-green algae) such as 3D imaging, spectral imaging, microscopic spectroscopy, and fluorescence recovery after photobleaching (FRAP). Cyanobacteria were chosen as a model microorganism due to their great importance for different scientific and biotechnological applications. Cyanobacteria are the most ancient photosynthetic microorganisms on Earth. Nowadays, cyanobacteria are one of the most wide-spreaded organisms in nature, and the ecological aspect in their investigation is quite valuable. On the other hand, thousand strains belonging to different species are cultivated in biolaboratories all over the world for different biotechnological applications such as biofuel cells, food production, pharmaceuticals, fertilizers, etc. Thus, the noninvasive spectroscopic methods are quite important for monitoring of physiological state of cyanobacterial cultures and other photosynthetic microorganisms.

**Keywords:** confocal laser scanning microscopy, fluorescent microscopic spectroscopy, spectral imaging, 3D bio-imaging, cyanobacteria, blue-green algae, photosynthetic system, photoactive pigment, light-harvesting complex
