Endophytic microorganisms isolated from the tissues of healthy sugar beets from Changji and Shihezi district in Xinjiang province were identified and investigated. The results showed that most of endophytic microorganisms of sugar beets belong to bacteria, in which Pseudomonas sp. and Bacillus sp. were the dominant communities with isolation frequency of 33.2%-59.2% and 12.7%-28.1%, respectively. The endophytic microorganisms were displayed a wide diversity by comparison their 16S rDNA and ITS sequences with GenBank using Blast software and analysis of phylogenetic tree. The biodiversity of endophytic microorganisms in roots of sugar beets were more than those of leaves, and the species of endophytic microorganisms in sugar beets from Changji district were more than those of Shihezi district. More endophytic microorganisms were isolated from poor growing seedlings and susceptible sugar beet cultivars than from the disease resistant counterparts. Endophytic microorganisms have been successfully re-isolated after inoculating sugar beet seedlings, in which endophytic microorganisms could colonize interior of the sugar beet roots by observation with scanning electron microscopy.