A r t i c l e s Theobroma cacao L. is a diploid tree fruit species (2n = 2x = 20 (ref. 1)) endemic to the South American rainforests. Cocoa was domesticated approximately 3,000 years ago 2 in Central America 3. The Criollo cocoa variety, having a nearly unique and homozygous genotype, was among the first to be cultivated 4. Criollo is now one of the two cocoa varieties providing fine flavor chocolate. However, due to its poor agronomic performance and disease susceptibility, more vigorous hybrids created with foreign (Forastero) genotypes have been introduced. These hybrids, named Trinitario, are now widely cultivated 5. Here we report the sequence of a Belizean Criollo plant 6. Consumers have shown an increased interest for high-quality chocolate, and for dark chocolate, containing a higher percentage of cocoa 7. Fine-cocoa production is nevertheless estimated to be less than 5% of the world cocoa production due to the low productivity and disease susceptibility of the traditional fine-flavor cocoa varieties. Therefore, breeding of improved Criollo varieties is important for sustainable production of fine-flavor cocoa. 3.7 million tons of cocoa are produced annually (see URLs). However, fungal, oomycete and viral diseases, as well as insect pests, are responsible for an estimated 30% of harvest losses (see URLs). Like many other tropical crops, knowledge of T. cacao genetics and genomics is limited. To accelerate progress in cocoa breeding and the understanding of its biochemistry, we sequenced and analyzed the genome

Criollo cacao (Theobroma cacao ssp. cacao) was cultivated by the Mayas over 1500 years ago. It has been suggested that Criollo cacao originated in Central America and that it evolved independently from the cacao populations in the Amazon basin. Cacao populations from the Amazon basin are included in the second morphogeographic group: Forastero, and assigned to T. cacao ssp. sphaerocarpum. To gain further insight into the origin and genetic basis of Criollo cacao from Central America, RFLP and microsatellite analyses were performed on a sample that avoided mixing pure Criollo individuals with individuals classified as Criollo but which might have been introgressed with Forastero genes. We distinguished these two types of individuals as Ancient and Modern Criollo. In contrast to previous studies, Ancient Criollo individuals formerly classified as 'wild', were found to

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