The microbial community composition in high arsenic groundwater aquifers was investigated by 454 pyrosequencing and illumina MiSeq sequencing approaches. Both groundwater and sediment samples were divided into low and high arsenic groups according to principal component analysis and hierarchical clustering. Microbial communities were significantly different among samples with different geochemistry. Predominant populations were Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella in high reducing area, Alishewanella, Psychrobacter, Methylotenera and Crenothrix in agricultural area, and Thiobacillus, Pseudomonas and Hydrogenophaga in high arsenic sediments. Arsenic, TOC, NH+ 4, Fe(II) and SO2- 4 were important factors shaping indigenous microbial communities.