Significance Glycosyl groups function as essential chemical mediators of molecular interactions in cells and on cellular surfaces. Microbes integrate carbohydrates into secondary metabolism to produce glycosylated natural products (GNPs) that may function in chemical communication and defense. Many glycosylated metabolites are important pharmaceutical agents. Herein, we introduce glycogenomics as a new genome-mining method that links metabolomics and genomics for the rapid identification and characterization of bioactive microbial GNPs. Glycogenomics identifies glycosyl groups in microbial metabolomes by tandem mass spectrometry and links this chemical signature through a glycogenetic code to glycosylation genes in a microbial genome. As a proof of principle, we report the discovery of arenimycin B from a marine actinobacterium as a new antibiotic active against multidrug-resistant Staphylococcus aureus .