Microorganisms are continuously blown onto the glacier snow, and thus the glacial depth profiles provide excellent geographic archives of the microbial communities. However, it is uncertain about how the microbial communities respond to the climatic and environmental changes over the glacier ice. In the present study, the live microbial density, stable isotopic ratios, 18O/16O in the precipitation, and mineral particle concentrations along the glacial depth profiles were collected from ice cores from the Muztagata glacier and the Dunde ice cap. Six bacterial 16S rRNA gene clone libraries were established from the Dunde ice core. The Muztagata ice core presented seasonal response patterns for both live and total cell density with high cell density occurring in the warming spring and summer. Both ice core data showed a frequent association of dust and microorganisms in the ice. Genera Polaromas sp., Pedobacter sp, Flavobacterium sp., Cryobacteriium sp., and Propionibacterium/Blastococcus sp. frequently appeared at the six tested ice layers, and constituted the dominant species endemic to the Dunde ice cap, whereas some genera such as Rhodoferax sp., Variovorax sp., Sphingobacterium sp., Cyanobacterium sp., Knoellia sp., and Luteolibacter sp. rarely presented in the ice. In conclusion, data present a discrete increase of microbial cell density in the warming seasons and biogeography of the microbial communities associated with the predominance of a few endemic groups in the local glacial regions. This reinforces our hypothesis of dust-borne and post-deposition being the main agents interactively controlling microbial load in the glacier ice.