MOTIVATION: Genome-scale metabolic reconstructions have been assembled for thousands of organisms using a wide range of tools. However, metabolite annotations, required to compare and link metabolites between reconstructions, remain incomplete. Here, we aim to further extend metabolite annotation coverage using various databases and chemoinformatic approaches. RESULTS: We developed a COBRA toolbox extension, deemed MetaboAnnotator, which facilitates the comprehensive annotation of metabolites with database independent and dependent identifiers, obtains molecular structure files, and calculates metabolite formula and charge at pH 7.2. The resulting metabolite annotations allow for subsequent cross-mapping between reconstructions and mapping of, e.g., metabolomic data. AVAILABILITY AND IMPLEMENTATION: MetaboAnnotator and tutorials are freely available at https://github.com/opencobra. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.