Seventy-two strains of endophytic fungi were isolated from the healthy bark, branches and leaves of Cephalotaxus hainanensis L.. Sixty-eight of them were morphologically classified into Fungi Imperfecti, thirty-three sporulated were identified to five genera. For those did not sporulate, one was identified to Rhizoctonia sp., the rest were tentatively classified into Mycelia Sterilia. Four were identified to Basidiomycetes. The result indicated the endophytic fungi of C. hainanensis show a degree of tissue specificity. There were significant differences about the quantity, genera and composition between the fungi isolated from bark and those from branches and leaves.