The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.