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In the coastal saline lakes on the White Sea shore different water layers overlay: surface aerobic and anoxic strata with a transition zone (chemocline) between them. In the deeper part of the salt aerobic stratum and in the chemocline, phototrophic microorganisms often form colored layers of 10-15 cm thickness. We investigated thin colored layers in five stratified lakes at the different stages of their isolation from the Sea using absorption and fluorescence spectroscopy, photobiology (measurements of primary photochemistry and photosystem II activity), and optical microscopy. The upper thin colored layer located in the aerobic strata (around 1,5 m depth) is greenish in all the lakes due to presence of unicellular algae containing chlorophyll a. Few decimeters below is located the oxic-anoxic interface colored in bright green, red or pink with dominating mixotrophic flagellates (Rhodomonas sp., Cryptomonas sp., Euglena sp.). A bit deeper, in the reduced zone of the chemocline dense green or brown cultures of anoxygenic phototrophs (green sulfur bacteria) appear, decreasing in concentration down to the lake bottom. The chemocline environment is characterized by lessened sunlight, high concentration of nutrients, and the presence of H2S. The photosynthetic apparatus of algae associated with the chemocline is characterized by high values of maximum quantum yield of primary photochemistry, activity of electron transport, photosynthetic performance of photosystem II, fraction of the active centers and low values of heat dissipation. The functional status of photosynthetic apparatus of cryptophytae algae, chemocline habitants, was found more efficient than that of green algae living in the aerobic layer. The work was supported by the Russian Foundation for Basic Research, project no. 16-05-00548a.