Quinoa (Chenopodium quinoa) is a high-protein, broadleaf seed crop in the Andes Mountains of Bolivia-Peru. It is an important dietary staple of hundreds of thousands of mostly Aymara and Quechua Indians in this region. Within the northern and central part of its range in the Andean valleys and Titicaca region, quinoa is threatened by regular outbreaks of downy mildew (Peronospora farinosa). As a result, the Bolivian quinoa breeding program of the PROINPA Foundation and researchers at BYU, through a McKnight Foundation Collaborative Crops Research Program (CCRP) grant, are investigating the use of molecular markers as alternative selection criteria for incorporating downy mildew resistance into new varieties being bred for the affected region. In the present study we are using degenerate primers designed from cloned resistance genes to amplify resistance gene analogs (RGAs) in quinoa. We have successfully cloned and sequenced 40 RGAs using this approach. Sequence comparison and Southern-blot analysis clearly distinguished seven classes of RGA. A bacterial artificial chromosome library of quinoa DNA was hybridized using probes specific to each of the seven classes and individual BAC clones for each of the RGA classes have been isolated. To determine the relationship of these RGAs, we have initiated the incorporation of several of the quinoa RGAs onto a recent quinoa genetic map based on SSRs. The candidate RGAs isolated in this study and their localization by genetic mapping should greatly facilitate the molecular cloning and analysis of disease resistance genes in quinoa in the future.