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International audienceArabica coffee is a major agricultural commodity worldwide, representing 60 % of the world’s coffee production. Arabica coffee is cultivated in more than 36 countries and is a key cash crop for many developing countries. Despite the coffee’s huge economic importance, there is very limited knowledge on the association of arbuscular mycorrhizal fungi with coffee roots. Therefore, we assessed the mycorrhizal diversity and community composition in Arabica coffee (Coffea arabica L.), using 454 pyrosequencing, in its Ethiopian center of origin. We studied the five most common coffee management systems in Ethiopia. Using pyrosequencing, we retrieved 10,061 mycorrhizae sequences across 30 samples, generating 36 operational taxonomic units from the four mycorrhizae orders: Glomerales, Diversisporales, Archaeosporales, and Paraglomerales; and eight families. Our results show that mycorrhizal diversity strongly differed between natural forest coffee systems and the other management systems. Furthermore, 13 operational taxonomic units were uniquely found in natural forest coffee. Finally, the mycorrhizal community composition in shade coffee plantations was different from the community composition in the other managed systems and the natural forest coffee systems. This is the first in depth study of mycorrhizal communities in wild coffee in its Ethiopian region of origin. Furthermore, we show for the first time the major differences in mycorrhizal communities in coffee between natural coffee forest and more intensively managed coffee systems. We, therefore, provide evidence of the conservation value of natural coffee forest systems as they harbor a unique mycorrhizal diversity, with possible future applications in low input coffee agriculture