Cocoa was domesticated two thousands of years ago by the Mayas and Aztecs in central America. The first varieties corresponded to Criollo types that give one of the finest chocolate. Many other diverse wild and more recently cultivated populations, named Forastero, exist in South America, in Guyanas and in Amazonia and Orinoco regions. Hybridizations between Criollo and Forastero types happened in the 18th century and resulted in Trinitario types. These vigorous hybrids were, then widespread in the original pure Criollo plantations, and in all the world. Molecular analyses showed that genome structure of modem Criollo varietes is similar to hybrid Trinitario. The Forastero and Criollo parents at the origin of modern Criollo and Trinitario were looked for. Around 90% of modern Criollo/Trinitario clones result apparently from hybridisation and subsequent introgressions between two genetically distant uniform types: homozygous Lower Amazon Forastero on one side and homozygous ancient Criollo varieties on the other side. Consequently, only the same two alleles are mainly found on each locus in the modem Criollo/Trinitario hybrid groups. A few number of generations (aroud six or seven) separates the first hybridisation step from actual modern Criollo/Trinitario varietes, and linkage desequilibrium must has been maintened between markers and genes of interest. This fact could enlarge considerably the applications of QTL analyses made recently in progenitors belonging to this group and related to many traits of interest like resistance, yield and quality. Molecular markers closely linked to these QTL could then be used to screen modern Criollo/Trinitario germplasm for important traits.