Abstract: To study the diversity of endophytic fungi isolated from Cephalotaxus hainanensis Li in Five Finger Mountain national nature reserve, 416 strains of endophytic fungi were isolated from 423 tissues. The strains were identified by their morphological characteristics and ITS-rDNA sequences. The 416 isolates belonged to 12 genera, 10 of which belonged to Fungi Imperfecti and 2 of which belonged to Ascomycetes. The results showed that Colletotrichum and Phomopsis were dominant species in different parts of C. hainanensis Li. Except for these two genera, Fusarium was the dominant specy in stems, while Lasiodiplodia was the dominant specy in roots and Didymostilbe was the dominant specy in leaves. And species diversity index (H') were 0.97-1.83. The similarity coefficient (CS) among different parts of C. hainanensis Li was 0.63-1.00. The similarities of ITS-rDNA sequences of strains WZS7165, WZS7240 and WZS7277 to the most closely related sequences in GenBank were 97%, 92% and 88%, respectively, which might be potential new species.