Vertical distribution of bacterial communities was detected in high arsenic (As) sediments in a representative high As area in Inner Mongolia. Nineteen sediment samples were collected from a 30 m borehole and detected by geochemistry and molecular ecological approaches including polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 16S rRNA gene clone library and 454 pyrosequencing. As contents ranged from 42.1 to 111.3 mg kg(-1) which fluctuated with different depth and significantly high in clay and mild clay sediment samples at depth of 8, 20, 25 and 28 m respectively. The ratios of As(III) to total As generally increased with depth but As(V) dominated in all sediment samples. High concentrations of total As, sulfur, iron and total organic carbon were generally found in clay and low in sand samples. Both DGGE patterns and 454 pyrosequencing results indicated that bacterial communities dynamically diversified with increasing depth and were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Chloroflexi. Most of the sediment samples were dominated by populations including Sporosarcina, Acinetobacter, Pseudomonas, Halomonas, Polaromonas, Paenibacillus and Flavobacterium. These populations were found with high similarities with those microbes capable of denitrification, sulfur oxidation, organic matter degradation and As resistance and reduction. These results implied that microbes might play an important role in As mobilization in the shallow aquifers of Hetao Plain, Inner Mongolia.