Abstract:Ninety-seven strains of endophytic fungi were isolated from the roots, stems and leaves of natural Scutellaria baicalensis Georgi, in which, thirty-three from the living stage and sixty-four from the riping stage. They were classified as thirty-eight fungal genera in which Alternaria is the dominant genus. The distribution of genera in riping stage was more diversified than that in living stage. The inhibitory activity screening was conducted with fourteen species of microbes. The results showed that ninety-one strains, accounting for 95.8% of all the isolates, showed inhibitory activity to one indictor or more. Some endophytic fungi showed remarkable inhibitory activity to Escherichia coli CGMCC1.1103, Bacillus subtilis CGMCC1.769, Bacillus cereus ATCC1361, Enteropathogenic E. coli ATCC49105, Candida albicans ATCC10231, Pestalotiopsis microspora CNUMB2PM01. All fungal strains of endophytes obtained in this study showed no inhibitory activity to Staphyloccocus aureus CGMCC2.282 and Rhodotorula rubra ATCC12600.