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The stratified lakes are a special group of hydrological objects. In aquatic systems with abnormal circulation of water the anoxygenic phototrophic microorganisms, green sulfur bacteria (GSB), may be of a particular interest. GSB are divided into two types according to their pigmentation: green-coloured and brown-coloured bacteria. The optical properties of the pigments make possible the study of the properties of microorganisms using spectral methods. In this work we performed spectroscopic measurements for natural water samples taken in March 2017 from several relic lakes with stratified water layers: Trekhtzvetnoe, N. Ershovskoye, Lagoon on the Cape Zeleny and Bolshie Khruslomeny. We developed spectral method to found out the ratio of different strains of bacteria in natural water sample without its extraction by organic solvents. This algorithm includes fitting of the bacteriochlorophyll fluorescence spectrum excited at 440 nm by Gaussian curves. We found parameters of approximating curves for different types of bacteria: the fluorescence peak in the 740-820 nm region for brown-colored bacteria is fitted by Gaussian curve with maximum at 760 nm and bandwidth 57 nm; for brown-colored bacteria the Gaussian is centered at 745 nm and has a width of 46,5 nm. Depth distributions of GSB differing in pigmentation were plotted for studied lakes with stratified water structure. These results are important for further in situ detection of two types of bacteria. The work was supported by the Russian Foundation for Basic Research, project no. 16-05-00548a.