To explore the resource of endophytic actinomycete in Fritillaria unibracteata, and alleviate the shortage of F. unibracteata resource, using F. unibracteata as experimental materials which growth in the western Sichuan plateau and cut its healthy bulb. Pure culture, insert, TLC and Oxford cup were applied to observe the mycelial morphology, research the ability of producing alkaloid and its antibacterial activity. Totally, 14 endophytic actinomycete strains were isolated by using Gao culture media. Based on the color reaction, 5 typical strains were selected for producing alkaloid. Through the TLC technique, all strains produced 2 obvious alkaloids spots. Antibacterial activity determination showed that the antimicrobial effects of 2 strains is prominent, the diameter up to 11 mm.16S rRNA gene sequence comparison analysis showed that 5 strains belonging to the Streptomyces. The alkaloids produced by endophytic actinomycetes are not related to F. unibracteata, but its fermentation liquid has antibacterial effect, it is worthy of further study.