Abstract Anoectochilus roxburghii (Wall.) Lindl is a traditional Chinese medicine, which has been used for diabetes and tumor treatment. The wild A. roxburghii and its endophytes live together to form a balanced symbiotic system. The endophytes produce various secondary metabolites to protect the host from being attacked by fungi and pests. Endophytes are rich bio-resources. Because of a major limitation of isolation methods and cultivation media, the diversity endophytes still remain undiscovered. Metagenomics simultaneous study of endophytes genomes from environmental samples may avoid the limitations of culture-dependent methods. We enriched the microbiota from the root of A. roxburghii and extracted and purified the metagenomic DNA.16S rDNA fragments were amplified by PCR and cloned to Escherichia coli DH5α to sequence. The endophytes were mainly uncultured bacterium, uncultured compost bacterium, Enterobacteriaceae, Paenibacillus sp., Bacillus sp. and Brevibacillus sp., according to 16S rDNA information. This research provided the basis for mining endophytes resources of A. roxburghii. Analyzed the groups of endophytes by partial sequence of 16S rDNA. This work opens further insight into the great potential of A. roxburghii microbiota.
