microbeMASST is a taxonomically informed mass spectrometry (MS) search tool designed to address the challenge of limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of over 60,000 microbial monocultures, users can search MS/MS spectra and link them to their respective microbial producers based on MS/MS fragmentation patterns. This tool enhances the understanding of microorganisms' roles in ecology and human health by identifying microbe-derived metabolites and their producers without prior knowledge. The microbeMASST reference database includes microorganisms isolated from various environments and categorized according to the NCBI taxonomy. The tool uses the Fast Search Tool to improve search speed and provides interactive taxonomic trees for easy interpretation. Users can perform batch searches using formatted MS/MS files or Universal Spectrum Identifiers (USIs). The web app displays query results in interactive taxonomic trees, which can be downloaded as HTML files. The tool has been validated through examples of medically relevant small molecules and has been applied to extract microbial information from metabolomics studies of mouse and human datasets. microbeMASST is expected to be a valuable resource for enhancing the understanding of microbial metabolites across various ecosystems and applications.microbeMASST is a taxonomically informed mass spectrometry (MS) search tool designed to address the challenge of limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of over 60,000 microbial monocultures, users can search MS/MS spectra and link them to their respective microbial producers based on MS/MS fragmentation patterns. This tool enhances the understanding of microorganisms' roles in ecology and human health by identifying microbe-derived metabolites and their producers without prior knowledge. The microbeMASST reference database includes microorganisms isolated from various environments and categorized according to the NCBI taxonomy. The tool uses the Fast Search Tool to improve search speed and provides interactive taxonomic trees for easy interpretation. Users can perform batch searches using formatted MS/MS files or Universal Spectrum Identifiers (USIs). The web app displays query results in interactive taxonomic trees, which can be downloaded as HTML files. The tool has been validated through examples of medically relevant small molecules and has been applied to extract microbial information from metabolomics studies of mouse and human datasets. microbeMASST is expected to be a valuable resource for enhancing the understanding of microbial metabolites across various ecosystems and applications.