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The coffee species Coffea arabica is facing numerous challenges regarding climate change, pests and disease pressure. Improved varieties will be part of the solution. Making optimal use of the scarce genetic diversity of the species is hence essential. In this paper, we present the first study of C. arabica genetic diversity covering its complete native habitat in Ethiopia together with its main domestication centers: Yemen and Hararghe region in Ethiopia. All in all, 555 samples were analyzed with a set of Single Sequence Repeat markers. Through admixture genetic analysis, six clusters were identified. A total of two "Core Ethiopian" clusters did not participate in the domestication of the species. There were four clusters that were part of the "Domestication Pathway" of C. arabica. The first one was named "Ethiopian Legacy" as it represents the genetic link between "Core Ethiopia" and the "Domestication Pathway" in Yemen and Hararghe. The geographic origin of this cluster in Ethiopia was the south of Ethiopia, namely Gedio, Guji and Sidama, which hence appears as the source of coffee seeds that led to the domestication of C. arabica. In Yemen, in addition to the "Ethiopian Legacy" cluster, we confirmed the "Typica/Bourbon" and "New-Yemen" clusters. In Hararghe, the "Harrar" cluster, never described before, likely originates from a re-introduction of domesticated coffee from Yemen into this region of Ethiopia. Cultivated varieties around the world today originate from the "Ethiopian Legacy" and "Typica/Bourbon" clusters and but none are related to the "new-Yemen" and "Harrar" clusters. Implications for breeding strategies are discussed. [ABSTRACT FROM AUTHOR]