Abstract Spatial isolation is currently thought to represent one of the major factors resulting in bacteria genetic variation and population abundance. The bacterial diversity in a distinct environment Zoige Alpine Wetland located in the northeast of the Qinghai-Tibetan Plateau with the altitude 3400 m on average aroused our great attention. This area belongs to Qinghai-Tibetan cold climate zone with the mean annual temperature about 1 °C. Although several studies on bacterial diversity in Qinghai-Tibetan Plateau had been reported, there is no report on wetland water in this area. In this work, six water samples were collected and the water qualities including COD Cr, NH 4 + -N, NO 3 - -N, NO 2 - -N , TN, TP, TOC were investigated, of which results indicated that more than 80% samples sorted as II–V class of surface water sources according to the National Water Quality Standard of China (GB3838-2002). Comparison of bacterial communities among the six samples was analyzed by DGGE of PCR-amplified 16S rDNA with universal bacterial primer sets. The profiles demonstrated that samples from the Flower Lake had more DNA bands than the Conservatory Station inferring higher diversity. In addition, the samples from the same environment shared similar compositions of bacterial communities. Bacterial community composition and predominant bacteria were analyzed by 16S rDNA clone library. The dominant group was Proteobacteria (51.6% of the total clones, which contained 24.2% alpha proteobacteria, 14.5% beta proteobacteria and 12.9% gamma proteobacteria). And the Bacteroidetes added to 17.7%, Verrucomicrobia to 4.8%. More than 24.2% of the total clones showed high similarity to uncultured bacteria. The above work provides some information on bacterial diversity for special site of spatial isolation.