Systems biology approaches to bacteria require an integrated database and a bioinformatics tool platform to enable automated and manual annotation, regulatory and metabolic network deduction, and the storage of related experimental as well as predicted data. In this context ROSY--the Roseobacter SYstems biology database--was developed for completed and draft genomes of representatives of the marine Roseobacter clade, which constitutes one of the most abundant bacterial clades in the ocean. ROSY provides an integrative view on comprehensive data collections such as KEGG, GenBank, RoseoBase, BRENDA, and PRODORIC as well as mediates the use of connected tools for promoter analysis (Virtual Footprint), genome and pathway visualization (CGView, PathCompare), and prediction of signal peptides (PrediSi). Moreover, metabolome, transcriptome, and proteome data can be stored in ROSY, supplying an integrated platform for comparative genomics and systems biology. This entire database system along with the data retrieval, comparative analysis, and website presentation tools (http://rosy.tu-bs.de) can be easily adopted for the systems biological analysis of other bacterial groups.