Since the discovery and clinical application of penicillin, microbial natural products have played a critical role in protecting public health. However, the emergence and wide spread of drug-resistant pathogens pose a new grave threat to humankind and make this issue one of the world's most severe public health problems. New chemical entries with antimicrobial activities, new mechanisms, or novel therapeutic methods are urgently needed for drug development. By exploring new sources, new technologies in separation and structural elucidation, genome mining, and synthetic biology, natural product research is entering a new golden age.This Special Issue on natural products with antimicrobial activities covers the discovery of new secondary metabolites, new mechanisms, and new therapeutic methods for potential application in antimicrobial drug screening and development.