Vertical distribution of the main bacteria isolated from the Muztagata ice core (about 22.4 m) was investigated by means of cultivation and 16S rRNA sequence analysis. The results showed that the amount of culturable bacteria fluctuated with ice core depth, and was more in dirty layer than in clean ice, which suggested the close corresponding relationship between high input of the bacteria deposited by wind and snowflow and dirty layer. Most of the bacteria were psychrophiles and psychrotolerants, including α- and γ-proteobacteria, Cryobacterium psychrophilum , CFB ( Cytophaga-Flavobacterium-Bacteroides ) group, high-G+C gram-positive bacteria (HGC). Acinetobacter sp. and HGC repeatly occurred in different ice depths, and their quantitative distribution was consistent with the change of the total amount of culturable bacteria with depth, which suggested the main bio-indicator; while Flavobacterium , Cryobacterium psychrophilum , and α-proteobacteria, also functioned as a secondary indicator of climatic and environmental changes. This study is the first report concerning continuous quantitative variation and pattern of the main culturable bacteria in ice core section.