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When studying meromictic (where is no mixing between layers of water due to differences in their density) reservoirs separating from the White Sea like the lagoon on Cape Zeleny, Lake Bolshie Khruslomeny, Lake Elovoe and Lake Trekhtsvetnoe, the problem often arises of determining the concentration of phototrophic microorganisms or their pigments in different layers of water. In the natural water of lakes separating from the sea in the White Sea region, at the border of the aerobic and anoxic zones, various anoxygenic phototrophic bacteria can be found, for example green and purple bacteria; therefore, several types of bacteriochlorophylls (BChl) can be simultaneously present in extracts prepared from natural water. In this work, an attempt was made for the first time to simultaneously determine the concentrations of two types of chlorosomal BChl (BChl d and BChl e) in pigment extracts using the fluorescence spectra.