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Microorganisms vary in both biomass and diversity composition along glacial depth profiles. However, it is not well known about the major processes controlling the structure diversity shift of microorganisms in a glacier, although, aeolian deposition has been widely accepted as one mechanism regulating the distribution of microorganisms in snow. To better understand the distribution of microorganisms in a glacier, variations in bacterial diversity and biomass along a pit profile from the Kuytun 51 Glacier in the Tianshan Mountains in China were investigated by using 16S rRNA gene library sequencing and flow cytometric analysis with cell sorting markers. Four clone libraries were established from each of the different sampling depths from the snow pit. A total of 311 insert clones were preliminarily screened by HaeIII-based amplified rRNA restriction analysis (ARDRA), and 83 representatives of the unique ARDRA patterns were sequenced. Sequence analysis showed that the bacteria in the snow pit were affiliated with 23 known subphyla within the members of the Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria phyla. To examine diversity shifts in snow, the diversity structures from the snow pit were also compared with those previously recovered from the different habitats along the Kuytun 51 Glacier surface and from the deep Malan Glacier. The results showed structure shift patterns in bacterial diversity among the surface, deep snow, and deep ice. Sequence analysis displayed a dramatic diversity shift from a mixture of Cyanobacteria and other eubacteria across the glacial surface to other eubacteria without Cyanobacteria in the deep snow. However, the biogeochemical analyses showed great variability in the measured abiotic and biotic components along the pit profile, which reinforced the idea of aeolian deposition being a dominant mechanism controlling the size and diversity of microorganisms in snow. Overall, the findings indicated a significant bacterial diversity shift between the surface and deep snow, confirming our hypothesis of a postdeposition influence on the microbial diversity structures in the glacier.