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The natural stratified reservoirs found in different stages of isolation from the White Sea are a special group of hydrological objects. Their origin and evolution are associated with the elevation of the Kandalaksha Bay coast with the speed of ~4 mm per year. In aquatic ecosystems with restricted water circulation the anoxygenic phototrophic microorganisms like green sulfur bacteria (GSB) may be of particular interest. These bacteria do not produce oxygen because they utilize hydrogen sulfide instead of water in the photosynthesis; they can habitat the anaerobic part of photic zone. Photosynthetic pigments of green sulfur bacteria are bacteriochlorophylls (BChls) and carotenoids. The optical properties of these pigments make possible studying of phototrophic microorganisms using spectral methods. We conducted the hydrological measurements and spectral analysis in several relic lakes located at the coast of the Kandalaksha Bay: Trekhtzvetnoe, N. Ershovskoye, Lagoon on the Cape Zeleny and Bolshie Khruslomeny. The comparison of the obtained results for natural water with the spectra of monocultures demonstrated the presence of GSB cells in anaerobic layers of the lakes near the chemocline and below. We developed spectral method to found out the ratio of two forms of GSB in water sampled from various depths. We found that deconvolution into three Gaussian curves fits well the shape of BChls fluorescence in GSB emission spectrum excited at 440 nm. The parameters of approximating curves vary for two forms of GSB: the wavelength of fluorescence maximum is ~760 and ~745 nm, the bandwidth (56,9 ± 1,4) and (46,5 ± 0,5) nm for green- and brown-colored bacteria respectively. This result was confirmed using an optical microscope and the data of the cell concentration; we estimated the number of BChl molecules per cell in each form of green sulfur bacteria.