In the past few years, genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus. An increasing number of expressed sequence tag (EST) data and genomic- or EST-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or genetic map based studies through the common use of ortholog loci across different species. Similar genomic information is available for tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I clade, integration of information on genetic markers would be possible and should lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality or adaptation. Our goal was to develop a comprehensive web data source for researchers working on Coffea genus, the Rubiaceae family or related species. MoccaDB (http://moccadb.mpl.ird.fr/) (Plechakova et al., 2009) is an interactive online database that manage information about EST-SSR and SSR markers. Markers were checked for redundancy, in vitro tested for cross-amplification and diversity over up to 38 Rubiaceae species. MoccaDB includes Cmap and BLAST tools and links to other related databases (e.g., SGN, NCBI). We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.