Laguna Verde ̵́s dome-shaped structures represent one of the most important Andean Microbial Ecosystems (AMEs) reported in the Central Andes. To date, this system lacks any kind of geomicrobiological research, so the following article represents the first study of these dome-shaped structures and their associated taxa. For this purpose, a chemical analysis of the water body, multiscale characterization of the domes, and analysis of the associated microorganisms were carried out. The lake’s alkaline waters rich in various minerals and its location at the margin of the Antofalla salt flat, fed by alluvial fans and hydrothermal input, provide favorable conditions for mineral precipitation and support for microorganism’s activity. Laguna Verde´s dome-shaped structures show an internal heterogeneous mesostructure composed of three zones: microcrystalline, organic (orange and green layers) and crystalline. The green layer of the organic zone is predominantly composed of Proteobacteria, Bacteroidetes, and Cyanobacteria, while the orange layer is mostly inhabited by Cyanobacteria. The results of the study suggest that oxygenic photosynthesis performed by Cyanobacteria is the main carbon fixation pathway in the microbial community, supported by carbon isotopic ratios of specific biomarkers. This finding highlights the important role that Cyanobacteria play in this ecosystem.