Aquilaria is a tree genus distributed in Southeast Asia, known for its oleoresin production. The induction of this oleoresin is described as a stress reaction by injury and, or fungal infection. In response to this stress, Aquilaria spp. produces an oleoresin that accumulates in the wood. The wood of not-injured trees is clear. The wood of injured trees tints and becomes odorous; we call it Agarwood. The quality of the oils, extracted from the wood, is variable. These variations are due to, in part, to the diversity of fungi that infect Aquilaria . The objective of this work is to characterize the fungal communities associated with Agarwood in areas where Aquilaria is native (South East Asia) and in an introductory area (French Guiana). We collected wood samples of Aquilaria from these countries to sequence fungal ITS2. Thus, we obtained 693,961 sequences grouped into 535 OTUs (Ascomycetes 87%, Basidiomycetes 10.5%). Fungi specific to a geographical area were highlighted as well as ubiquitous fungi in different areas. These results allow considering the role of these microorganisms in the quality of Agarwood.