Endophytic strain LD5 was isolated from the stems of Gentiana nubigena. The fermentation broth of LD5 showed antibiosis activities against Staphylococcus aureus and Escherichia coli. According to the characteristics of morphology, physiology and biochemistry tests and the comparison of 16S rDNA sequence, strain LD5 was identified as Bacillus amyloliquefaciens. Strain LD5 could produce flavonoids, gentiopicroside, and a kind of analogue of alcoholic extract from Gentiana nubigena.