Abstract: The microstructure and distribution of endophytic fungi in Maytenus confertiflorus root were studied by permanent paraffin sectioning and microscope photography. The secondary structure of the root consisted of periderm and vascular cylinders. Periderm was composed of cork, cork cambium, and phelloderm. The cork consisted of five or six layers of long cells. The secondary phloem occupied 46% of the diameter of the root and the parenchymas cells had abundant inclusions. The secondary xylem consisted of vessels, and xylary radial and some xylary parenchyma cells. Some segments of hypha, swelled hypha, pelotons and conidiophore were in colonies in cork and secondary phloem. Endophytic fungi existed in the local cells of cork and secondary phloem in the root.