 WebMGA is a web server designed to provide researchers with a platform for fast and efficient metagenomic data analysis. It contains more than 20 tools including ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminants, taxonomic analysis and functional annotation. Researchers can use WebMGA either through web browsers or programming scripts to conduct individual analyses or to configure and run customized pipelines. WebMGA is free and open source, making it accessible to all researchers. This article was authored by Nio Beifang, Fu Liming, Zhu Zhengwei and others.