Simple SummaryA comprehensive geochemical, mineralogical and microbiological analysis of bottom sediments was carried out in five main areas of the littoral zone of Lake Issyk-Kul, one of the largest mountain lakes in the world. The aim of this work is to study the microbial diversity of bottom sediments of Lake Issyk-Kul and to establish the role of microbiota in biogeochemical processes, in particular, its involvement in authigenic mineral formation. Aerobic and anaerobic oxidation of organic matter begins at the water-sediment interface and is the main source of carbon dioxide which provides the formation of carbonate minerals. Oxygen consumption during organic carbon oxidation triggers anaerobic sulphate reduction processes, leading to the formation of authigenic sulphide minerals. This work is the initial stage in the study of the microbiology and biogeochemistry of the ecosystem of Lake Issyk-Kul, and the data obtained will allow a better understanding of the processes of C, N and S cycling in the lake and the mechanisms of formation of modern bottom sediments.AbstractThis article presents geochemical, mineralogical and microbiological characteristics of five samples of modern bottom sediments in the littoral zone of the high-mountain salty lake Issyk-Kul. The 16S rRNA gene sequencing method shows that the microbial community consists of organic carbon degraders (representatives of phyla:Proteobacteria,Chloroflexi,BacteroidotaandVerrucomicrobiotaand familiesAnaerolineaceaeandHungateiclostridiaceae), photosynthetic microorganisms (representatives ofChloroflexi, phototrophicAcidobacteria, purple sulphur bacteriaChromatiaceaeand cyanobacteria) and bacteria of the reducing branches of the sulphur biogeochemical cycle (representatives ofDesulfobacterota,DesulfosarcinaceaeandDesulfocapsaceae). The participation of microorganisms in processes in the formation of a number of authigenic minerals (calcite, framboidal pyrite, barite and amorphous Si) is established. The high diversity of microbial communities indicates the presence of labile organic components involved in modern biogeochemical processes in sediments. The active destruction of organic matter begins at the water-sediment interface.