The Neotropic deserts comprise three continental deserts (Low Monte, High Monte, and Central Andean Dry Puna), and two coastal deserts (Atacama and Sechura deserts, Figure 4.5). They cover 1.1 million square kilometres, of which only 6 per cent receives legal protection. Their mean population density is 18 persons per square kilometre, and their mean human footprint (16) is lower than in their North American counterparts, with most pressure concentrating in the Sechura Desert in the coasts of Peru. These deserts form a long arid continuum that cover South America's "arid diagonal", starting from the Pacific Ocean just south of the equator in Peru, and running in a southeast direction to the Atlantic coast of northern Patagonia, at latitude 43°S.

The barren landscape of the Atacama Desert features one of the driest deserts on earth. The almost complete absence of vegetation in its interior is due to the lack of precipitation and the high mineral content of the soils. Rare rainfall events cause ephemeral plants to germinate and burst with flowers for a short period of time. The Monte, east of the Andes, is a fold desert with sandy plains, plateaus, and rocky foothills with an open, low thorn-scrub harbouring a characteristic endemic flora of zygophylls (family Zygophyllaceae). There are also edaphic communities of many species such as Prosopis thickets in ravines, shrub lands of broom rape (Baccharis) and saltbush (Atriplex) on clay soils, and Allenrolfea vaginata and Suaeda divaricata in salty soils. The dry Central Andean Puna carries tall tussocks of bunchgrass and other high-altitude grasses, shrubs like Parasthrephia lepydophilla and Baccharis, and a unique flora of high-altitude cushion plants. The main land use in the Puna is grazing with llamas, alpacas, goats and sheep. In ancient, pre-Hispanic times, these deserts were an important part of the Inca Empire; a network of roads stretched through them forming the Qhapaq ñan, or Camino del Inca (the Inca Road).