antiSMASH 3.0 is a comprehensive resource for genome mining of biosynthetic gene clusters (BGCs). It was introduced in 2011 as a web server and standalone tool for the automatic identification and analysis of BGCs. Version 3.0 includes major improvements, such as integration with the ClusterFinder algorithm, which allows probabilistic detection of unknown types of BGCs. It also includes a new dereplication module that compares identified BGCs with known clusters, improving the identification of novel BGCs. The tool now identifies and annotates active sites of key biosynthetic enzymes, and improves chemical structure prediction by incorporating polyketide reduction states. Additionally, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. The tool also includes improved nomenclature and detection of RiPPs and polyketides, as well as updates to the back-end and library to enhance flexibility and speed. antiSMASH 3.0 is now more comprehensive and will be useful for the discovery of new secondary metabolites and metabolic engineering. The tool is available at http://antismash.secondarymetabolites.org and is free and open to all users.antiSMASH 3.0 is a comprehensive resource for genome mining of biosynthetic gene clusters (BGCs). It was introduced in 2011 as a web server and standalone tool for the automatic identification and analysis of BGCs. Version 3.0 includes major improvements, such as integration with the ClusterFinder algorithm, which allows probabilistic detection of unknown types of BGCs. It also includes a new dereplication module that compares identified BGCs with known clusters, improving the identification of novel BGCs. The tool now identifies and annotates active sites of key biosynthetic enzymes, and improves chemical structure prediction by incorporating polyketide reduction states. Additionally, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. The tool also includes improved nomenclature and detection of RiPPs and polyketides, as well as updates to the back-end and library to enhance flexibility and speed. antiSMASH 3.0 is now more comprehensive and will be useful for the discovery of new secondary metabolites and metabolic engineering. The tool is available at http://antismash.secondarymetabolites.org and is free and open to all users.