Aims:  Shanyin County is one of the most severe endemic arsenism affected areas in China but micro‐organisms that potentially release arsenic from sediments to groundwater have not been studied. Our aim was to identify bacteria with the potential to metabolize or transform arsenic in the sediments. Methods and Results:  Culture and nonculture‐based molecular methods were performed to identify arsenite‐oxidizing bacteria, arsenate‐reducing bacteria and arsenite oxidase genes. Arsenite‐oxidizing bacteria were identified only from the land surface to 7 m underground that were affiliated to α‐ and β‐Proteobacteria. Arsenate‐reducing bacteria were found in almost all the sediment samples with different depths (0–41 m) and mainly belong to γ‐Proteobacteria. Several novel arsenite oxidase genes (aoxBs) were identified from the upper layers of the sediments (0–7 m) and were found to be specific for arsenite‐oxidizing bacteria. Conclusions:  The distribution of arsenite‐oxidizing bacteria in upper layers and arsenate‐reducing bacteria in different depths of the sediments may impact the arsenic release into the nearby tubewell groundwater. Significance and Impact of the Study:  This study provides valuable sources of micro‐organisms (and genes) that may contribute to groundwater arsenic abnormality and may be useful to clean arsenic contaminated groundwater.

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