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Six Rutaceae species collected from natural habitats (Malta, Mallorca (Spain), and Tenerife (Spain)) and the Botanical Garden in Marburg were examined with respect to mycorrhizal structures and fungal identity. All species have the same gross colonization pattern of arbuscular mycorrhiza (AM) with distinct intracellular and intercellular phases but show remarkable differences in details, especially in terms of the extent of the intracellular phase. The associated AM fungi, identified using molecular methods, cluster together with Glomus hoi Berch & Trappe, although the plants were collected from very distant locations.