Microbial functional potential in high arsenic (As) groundwater remains largely unknown. In this study, the microbial community functional composition of high arsenic groundwater samples from Hetao Basin, China, was investigated using integrated methods including DGGE, gene clone library, qPCR, and GeoChip. The results showed that As-related genes (arsC and arrA), sulfate-related genes (dsrA and dsrB), and methanogen genes (mcrA) were correlated with As, SO2- 4, or CH4 concentrations in groundwater, respectively. Arsenic, total organic content, SO2- 4, NH+ 4, oxidation-reduction potential (ORP), and pH were important factors shaping the functional microbial community structure. Alkaline and reducing conditions associated with microbially-mediated geochemical processes could be linked to As enrichment in groundwater.