A total of 67 strains of endophytic fungi were isolated from roots, branches and leaves in Dendrobium officinale. These strains were identified into 16 genera based on morphological characters and ribosomal DNA(rDNA) sequence analysis, thereinto Fusarium and Alternaria are dominant populations in D. officinale. From analysis results we found some endophytic fungi show a certain degree of host and tissue preference. The research provided theoretical basis for developing and utilizing the resources of endophytic fungi in Dendrobium.