Simple SummaryThe Laguna Negra is a high-altitude hypersaline lake located in the Puna region in Argentina, hosting microbial mats and modern stromatolites, microbially formed rocks found throughout the geological record. Some recent studies have shown the relevance of the lakes in this region for (i) the discovery of new extremophiles, particularly those tolerant to high UV and, furthermore, (ii) the study of biosignatures in stromatolites. In this work, a detailed survey, layer by layer, of the microbial diversity of the most widespread microbial mat in the Laguna Negra was reported, to unravel the spatial arrangement of the microbial community. The results reveal the vertical distribution of the main prokaryotic microbial taxa, and underline abundant Deinococcus-Thermus at the top of the microbial mat with high amounts of deinoxanthin, which may help the total community to cope with high UV radiation. This study allows a better understanding of the community strategies to thrive under environmental stressors in the Laguna Negra and its counterparts in the Altiplano-Puna region. The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.