Culturable endophytic bacteria were isolated from medicinal plant Ilex cornuta by platespreading method, strains with strong inhibitory effect on phytopathogen were screened by confrontation culture and fermentation filtrate culture methods, and the morphological changes of phytopathogen hyphae treated with endophytic bacteria were examined by microscopy and micrograph. Their phylogenetic relationships were determined by homology analysis of the 16S rDNA sequences of PCR products and the taxonomic status of the selected strains was determined based on their morphology, physiology, biochemical test results and 16S rDNA sequence analysis. A total of 85 endophytic bacteria were isolated from the healthy roots, stems, leaves and fruits of I. cornuta, and 10 strains of them showed strong inhibitory effect on Alternaria alternata, Magnaporthe grisea, Fusarium oxysporum, and were preliminarily identified belonging to four genera and seven species. Three strains with the strongest inhibitory effect, GG78 (60.3%), GG31 (48.1%) and GG13 (61.0%) belonged to Enterobacter cloacae, Enterobacter ludwigii and Bacillus cereus, respectively. Microscopic analyses showed that the inhibited phytopathogen hyphae became deformed, distorted, and partially expanded forming plasma concentration and hairlike branch on the hyphae base. These morphological changes could be caused by the extracellular metabolic substances secreted by the endophytic bacteria, such as antibiotics, hydrolytic enzymes, alkaloids and so on.