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The rates of oxygenic and anoxygenic photosynthesis, the microorganisms responsible for these processes, and the hydrochemical characteristics of the sulfide-containing karst lakes, Black Kichier and Big Kichier (Mari El Republic), were investigated. In these lakes, a plate of anoxygenic phototrophic bacteria (APB) is formed at the upper boundary of sulfide occurrence in the water. The phototrophic community of the chemocline zone was analyzed using a combination of high-throughput sequencing of the 16S rRNA gene fragments and light and electron microscopic techniques. Green-colored <i>Chlorobium clathratiforme</i> were absolutely predominant in both lakes. The minor components included green sulfur bacteria (GSB) <i>Chlorobium</i> spp., symbiotic consortia <i>Chlorochromatium magnum</i> and <i>Pelochromatium roseum</i>, purple sulfur bacteria (PSB) <i>Chromatium okenii</i>, and unidentified phylotypes of the family <i>Chromatiaceae</i>, as well as members of the <i>Chloroflexota</i>: <i>Chloronema</i> sp. and <i>Oscillochloris</i> sp. Based on the results of the molecular analysis, the taxonomic status of <i>Ancalochloris perfilievii</i> and other prosthecate GSB, as well as of the PSB <i>Thiopedia rosea</i>, which were visually revealed in the studied freshwater lakes, is discussed.