In this paper, a bacterial endophytic strain SHEN20121 was isolated from the roots of Phyllostachys edulis, and displayed high bioactivity against plant pathogenic fungi. Appraising with the analyses of 16S rDNA sequencing, the similarities of sequence between the SHEN20121 strain and other 97 registered bacterial strains of Paenibacillus were 97%-99%. The sequence alignments and phylogenic analysis showed strain SHEN20121 was closely related to Paenibacillus polymyxa and the bootstrap value was 100. SHEN20121 strain was found to have a strong antibiotic activity against six pathogenic fungi including Fusaricum oxysporum, Alternaria alternate, Rhizoctonia solani, Botrvtis cinerea, Pestalotiopsis microspora and Penicillium italicum by the dual-culture test. Inhibitory effect on Botrvtis cinerea, Pestalotiopsis microspora, Penicillium italicum were particularly significant. It is the first report on the resistance of Paenibacillus polymyxa to Pestalotiopsismicrospora. We concluded that the active strain SHEN20121 has potential ability in restraining plant pathogens and would be exploited as an attractive origins of new drug discovery and plant defense activator in the future.