Chile, isolated by a hyper-arid desert in the north, the Andes Range to the east and the Pacific and Antarctic waters (west and south), has a highly endemic flora. This hotspot of biodiversity is in danger not only due to increasing desertification, but also because human activities can diminish agrobiodiversity. Quinoa (Chenopodium quinoa Willd.) is an Andean species producing highly nutritious grains, which almost disappeared from Chile during the Spanish colonization. Today less than 300 small-scale and highly isolated farmers still grow it as a rain-fed crop. This review describes the biogeographical-social context of quinoa in Chile, and its high genetic diversity as a product of a long domestication process, resulting in numerous local landraces whose conservation and use for breeding improved varieties is of paramount importance. We suggest the term "lighthouse crop" to emphasize its contribution to small scale ecological and bio diverse agriculture, particularly in stressful environments, to promote a healthier nutrition and more equitable markets in the world. Furthermore this crop and its exceptional nutritional properties were invoked by the United Nations Food and Agriculture Organization (FAO) to promote its use worldwide, and to declare 2013 the International Year of Quinoa.