Aquilaria is a tree species belonging to the family of the Thymeleaceae. When the tree is wounded, it can produce a blackened wood, also known as agarwood. The blackened wood has a darker colour than healthy wood and gives off a strong fragrance greatly appreciated by perfumers and by certain oriental religious communities. Production of this blackened wood is deemed to depend on environmental factors, including fungi. The purpose of this work was to set up an experiment in Régina and Cacao, in French Guiana, to characterize the organization of microbial communities, particularly fungi, associated with Aquilaria crassna Pierre ex Lecomte, in order to understand their roles in agarwood formation. In this study, we used mass sequencing with reversible terminators (Illlumina). Of the initial 120 samples from which DNA was extracted, 27 samples of healthy wood, 29 samples of wounded wood and 3 soil samples were kept. These 59 samples were used to generate an average 37,890 sequences per sample. After data processing, we used 921 unique sequences spread across these 59 samples. Some majority OTUs were found for the wood samples. The soil samples showed the same trend, along with greater OTU diversity. With a view to producing agarwood of controlled quality in experimental Aquilaria plantations in French Guiana, we determined the majority genera present in the wood of these trees before and after wounding, and some majority genera depending on the different plots in Cacao and Régina. The results indicated that some genera were common to each other and to the literature, but others were fairly characteristic of a specific geographical zone, such as Periconia for Régina and Paraphaeosphaeria for Cacao.