A searchable database documenting variation in ribosomal RNA operons in Bacteria and Archaea. The redesigned rrnDB brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing.