The presence of indigenous endophytic bacteria in tissue-cultured seedlings germinated from seeds of Zizyphus jujuba var. Fupingdazao was investigated using cultivation, light microscopy and scanning electronic microscopy (SEM). In addition, bacteria specific 16S rDNA PCR followed by denaturing gradient gel electrophoresis (DGGE) was used. No cultivable bacteria could be detected on plates or in liquid cultures. However, large quantities of endophytic bacteria in jujube seedlings were observed under the light microscope. The bacterial cells were round (measuring 1.5 μm -1.8 μm), short rods (2.2 μm -2.9 μm  1.1 μm -1.9 μm) and rod shaped (3.7 μm -4.4 μm  1.6 μm -1.9 μm). Rod-shaped bacterial cells (measuring 3.5 m -4.0 m  1.5 m -2.0 m) were observed by SEM as well. A 16S rDNA fragment of 1.5 kb could be amplified from the total DNA of seedlings of jujube using the bacterial primer pair 27F/1525R. The V3 fragment of 16S rDNA was separated by DGGE, and the 16S rDNA-PCR-DGGE showed that there were at least six dominant bands within the seedlings of Z. jujuba var. Fupingdazao. It can be concluded that endophytic bacteria that cannot be detected by cultivation are present with high densities in jujube seeds.