Abstract: As an epiphytic orchid, Cleisostoma williiamsonii is a very beautiful ornamental plant, and plays an important role in tropical forest ecosystems. In this paper, tissue culture method was used to isolate endophyte in root of wild C. williiamsonii from Bawangling, Hainan. The total 145 isolates were identified into 15 genera, including Penicillium 16 strains, Aspergillus 12 strains, Pestalotiopsis 5 strains, Fusarium 19 strains, Neonectria 2 strains, Chaetomium 4 strains, Calonectria 5 strains, Xylaria 5 strains, Paecilomyces 7 strains, Alternaria 2 strains, Phomopsis 8 strains, Colletotrichum 32 strains, Rhizopus 5 strains, Mucor 7 strains; Albugo 6 strains. Acorrding to the ITS sequences, another 10 strains needed more identification, which had low degree of similarity with Botryosphaeria sp., Beltraniella sp.. It showed that Colletotrichum sp., Penicillium sp., Fusarium sp. were the predominant species, and had the richest biodiversity in tropical coniferous forests.