In the 1970s a large proportion of the people of Western Sahara went into exile, settling as refugees in camps in Tindouf, Algeria. They took with them their traditional pastoralist way of life and their breeds of small ruminants, which formed the main part of their diet. Almost three decades later, these breeds, having endured the war and the exodus, are in danger of extinction, firstly because of their situation, and secondly because of scientific ignorance about them. In the present paper, we develop a genetic characterization of the Sidaun and Kerrian breeds of sheep and the Buzguender breed of goats in the Saharawi refugee camps. The results indicate that all the breeds studied still have a high level of genetic differentiation and are not showing signs of recent exotic gene migrations. This is encouraging, for it indicates that we are in time to conserve these genotypes of high ecological value for their capacity to survive in the desert.