Abstract: In this paper, 3 plant samples of Bletilla striata from diferent sites were collected in Nanhua County, Yunnan Province (HCN 1, HCN 2, HCN 3), and respective habitat recorded and soil sampled. The different species composition of endophytic fungi in the roots of B. striata was analyzed by high throughput sequencing technique. The results showed that Phyllosticta sp., Erysiphe sp., Podosphaera sp., Glomerella cingulata, Aspergillus sp., Rhodosporidium diobovatum and Sterigmatomyces halophilus were significantly different in species abundance and composition among sampling sites. It is speculated that Phyllosticta sp., Erysiphe sp., Podosphaera sp. and Glomerella cingulate were pathogenic fungi, whilst Aspergillus sp., Rhodosporidium diobovatum and Sterigmatomyces halophilus well-defined biocontrol fungi. The root of B. striata did not show visible disease symptoms possibly due to the existence of biocontrol fungi. In this study, sample distance, geographical location, and soil physical and chemical properties are the factors responsible for the difference in endophytic fungi composition in roots of B. striata. Among which, soil physical and chemical properties are the key factors.