Endophytic bacteria reside in most healthy plants; it can not be easily influenced by outer environment. Some endophytic bacteria are beneficial to host plants, such as growth promotion, disease prevention and nitrogen fixation etc. Therefore, endophytic bacteria are the potential microbial fungicides, it may be widely applied. In this study, endophytic bacteria were isolated from soybean cultivar Hefeng 25 that was a main soybean cultivar in Heilongjiang province, China. The results indicated that the density of endophytic bacteria varied in different tissues of the plant. It was 3.4×103 CFU/g in roots, 2.8×103 CFU/g in leaves, 2.9×102 CFU/g in stems and 1.4×102 CFU/g in seeds. The activity of 121 strains against Fusarium oxysporum f. sp. soybean, caused soybean root rot, were assayed. 25.6% of them showed antagonistic activity against F. oxysporum f. sp. soybean. One of them, strain TF28 isolated from soybean roots could inhibit the growth of many fungal pathogens. The inhibitory rates against F. oxysporum from different plant species were 80.2%-96.7%. Based on the morphological, physiological and biochemical characteristics as well as the sequence of 16S rRNA, strain TF28 was identified as Bacillus amyloliquefaciens.