BASys2 (Bacterial Annotation System 2.0) is a freely available powerful web server for comprehensive bacterial genome annotation. It identifies all gene types (protein-coding, tRNA, rRNA, etc.) and generates up to 62 annotation fields per gene using over 30 tools and 10 databases. The interactive genome viewer provides detailed, multi-resolution visualizations and clickable gene cards, while also supporting metabolome annotations and 3D protein structure visualizations. Annotations include structural, functional, and statistical data, with results available for download in JSON and GenBank formats. BASys2 delivers fast, extensive, and high-quality genome annotations that rival or exceed those in databases like UniProt.