Arsenic contamination in a water system is an urgent environmental problem that has caused severe endemic arsenicosis in south and southeast Asian countries. It is well known that microbially mediated arsenic metabolism can enhance arsenic mobility, bioavailability, and toxicity. Here, for the first time, we applied the Illumina high-throughput metagenomic and metatranscriptomic approaches to study the distribution, diversity, abundance, and expression of microbial arsenic metabolism genes in activated sludge and five coastal sediments. An average depth of similar to 2.6 Gb clean data for each sample was finally obtained for BLAST analysis after quality filtration and normalization. The results revealed that: (1) highly diverse arsenic metabolism-like genes were found and the overall abundance varied from 0.18 % to 0.26 % in the six metagenomic data sets; (2) arsenic metabolism-like genes were expressed with extremely low levels or no expression at all in activated sludge; and (3) the distribution, diversity, and abundance of aioA-like, arrA-like, arsB-like, ACR3-like, and arsM-like genes varied significantly in the six surveyed environments. This study provided a novel perspective on understanding the ecology of arsenic metabolism in different water environments using high-throughput sequencing technique.