Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe mediated As metabolism plays an important role in the global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 414,773 representative sequences from 59 As metabolism gene families, which are affiliated with 1,653 microbial genera from 46 phyla. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment, and soil). Compared with other databases, AsgeneDB substantially improved the mapping ratio of short read in metagenomes from various environments. Our results indicate that the diversity and importance of microbial arsenic metabolism in the environment remains to be explored. In addition, we developed an R package Asgene to facilitate the analysis and statistical of metagenomic data. AsgeneDB and the associated R Package Asgene will greatly promote the study of arsenic metabolism in microbial communities in various environments.