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Cyanobacteria are the model organisms for studying photosynthesis; their applications in ecotoxicological analysis are also suggested. Raman spectroscopy allows analyzing and comparison of chemical composition of the cyanobacteria strains and studying of the state and conformation of the molecules which participate in the living processes of cyanobacteria. In order to collect spectral information about different structural components of cyanobacterial cells, in the present work Raman spectra of the cyanobacterium Synechocystis sp. PCC 6803 mutants deficient in phycobiliproteins,which are parts of the light harvesting antenna of cyanobacteria, were measured and analyzed. The wild type of Synechocystis, CK mutant, and PAL mutant were grown for 4-5 days in liquid BG-11 medium at 30oC and white light intensity of 40 mmol photons m-2 s-1. The suspension of cyanobacteria in growth medium was placed into the quartz cuvette with a thickness 2 mm and the cuvette was positioned on the microscopic stage of InVia Raman spectrometer (Renishaw, GB) equipped with lasers with 785 nm and 1064 nm wavelengths. For the spectra acquisition the laser beam was focused inside the cuvette via objective N Plan 50/0.50 (Leica, Germany) with long working distance