Aquilaria microcarpa is one of agarwood-producing plants, Interaction of pathogenic fungi may cause physiological changes in plants that have an impact on visual changes in cells, tissues or organs of plants. This study aims to determine differences in the anatomical characters of Aquilaria microcarpa that have been inoculated with Fusarium sp. Observations of anatomical characters showed that traits of inoculated and un-inoculated Aquilaria microcarpa in general are partly different. The difference was found in wood color, odor/aroma, the pores of wood and leather inserted visible. Chemical compounds contained in the plant interact with fusarium was Elemol, Baimuxinal, 3-phenyl-2-butanone, chromen-4-one.