Self-fluorescence is a powerful tool for investigation of living photosynthetic microorganisms. Since the physiological state of such microorganisms is closely related to the operation and activity of photosynthetic system; thus, any variations in spectroscopic properties of their self-fluorescence indicate the changes in their physiological state. Cyanobacteria (or blue green alga) are one of the most widespread photosynthetic organisms in nature, and the ecological aspect in their investigation is quite valuable. On the other hand, thousands of strains belonging to different cyanobacterial species are cultivated in biolaboratories all over the world for different biotechnological applications such as biofuel cells, food production, pharmaceuticals, and fertilizers. Thus, the novel noninvasive methods of their investigation are quite important for on-line monitoring of cyanobacterial cultures. In this chapter, several fluorescence techniques are presented for investigation of living cyanobacterial cells and cultures.