Abstract: Taking medicinal plant Flos Lonicerae as experimental material, endophytic bacteria of different parts of root, stem and leaf were isolated and purified, cell features were determined by Gram dye and Spore dye methods. They were preliminary classified into two types （first type and second type） combined clony characteristic, physiological and biochemical characteristics. Microbes were counted by dilution spread method for different parts of F. lonicerae. Results indicated that distribution of endophytic bacteria total number in root was the most, leaf was second and stem was the least, it suggestted that distribution difference of endophytic bacteria in F. lonicerae was in accordance with different parts. Based on dye features, microscopic observation results and cultive characteristics, endophytic bacterial first type was accorded with genus Bacillus, and second type was accorded with characteristics of genus Paenibacillus.