To study the root microstructure and the distribution of the endophytic fungi in Taxus chinensis var. mairei.The roots of Taxus chinensis var. mairei at nature were cut with paraffin, dyed and observed by microscope.The secondary structure of the roots of Taxus chinensis var. mairei consisted of the periderm and vascular cylinder (stele). Axial and radial systems formed the secondary xylem of the roots. Tracheids and xylary parenchyma cells constituted the axial system, and xylary radial formed the radial systems. The secondary phloem consisted of sieve cells and phloem parenchymas. Only a small quantity of phloem fibers were distributed in the secondary phloem, and the phloem ray was unconspicuous. Many endophytic mycelia penetrated in the velamina.The secondary structure of the root of Taxus chinensis var. mairei accords with that of other gymnosperms and dicotyledons, although its secondary xylem is constituted with tracheids and sieve cells. The endophytic mycelia exists in the local cells of velamina in the roots of Taxus chinensis var. mairei.