CocoaGen DB is a Web portal that comprises molecular genetic, genomic and phenotypic data on cocoa. It was initiated through a collaborative project involving CIRAD (Centre de coopération internationale en recherche agronomique pour le développement, France), University of Reading (School of Plants Sciences, UK) and USDA-ARS (United States Department of Agriculture, USA). This database combines molecular genetic information from TropgeneDB (http://tropgenedb.cirad.fr) and phenotypic data from ICGD (International Cocoa Germplasm Database, http://www.icgd.reading.ac.uk). CocoaGen DB is available by internet (http://cocoagendb.cirad.fr). A user-friendly and intuitive web consultation interface allows to perform complex queries combining genetic and phenotypic information; for instance: 'Which clones are resistant to a particular disease and have specific alleles linked to a QTL related to another trait of interest (quality,...). The Comparative Map Viewer CMAP was linked to CocoaGen DB. Furthermore, we developed a Java applet tool for the visualization of clones genealogy and for alleles tracking. We created submission forms to simplify and standardize genomic data integration and to control their quality by the verification of identifiers and datatypes. To sum up, CocoaGen DB was specifically designed to allow end-users (breeders and/or molecular geneticists) to best exploit genetic and phenotypic information available on cocoa germplasm.