Aquilaria is a tree species belonging to the Thymeleaceae family. When Aquilaria sp. is injured, it produce agarwood. Agarwood is characterized by a darker wood colour than the healthy one and by a strong perfume that is much esteemed by perfumers and some oriental religious communities. The production of agarwood is presumed to depend of environmental factors, among them fungi. The aim of this work is to obtain an overview of fungi present in Aquilaria sp. from different countries. Aquilaria sp. is endemic to South East Asia including notably Cambodia, Laos and Thailand, where it is cultivated to produce agarwood. In French Guiana, native south East Asian farmers would like to locally produce agarwood in their field. That's why we wonder if fungal communities inducing agarwood are the same between these countries. NGS was used to characterize fungal communities associated with agarwood. 693,961 sequences that cover ITS2 estimated about 250 bp have been obtained. These sequences have been grouped into 535 OTUs, displaying 100% identity. 87 % were Ascomycetes and 10.5 % were Basidiomycetes. These results show differences in fungal communities between aboveground and belowground parts of the tree. Likewise differences between countries within fungal communities were also observed. Notwithstanding our results highlight common OTU between the different countries. Comparisons between aboveground parts and belowground parts and comparisons between different countries showed that several different fungal species may be responsible of the infection, other factors may disturb the community after infection and some samples may be not infected. From this study, some candidates potentially involved in agarwood production were selected. The role of these fungi in the induction of agarwood production will be further studied.