Cacao (Theobroma cacao L.) was cultivated by the Mayas over two thousand years ago. The type of cacao cultivated by the Mayas constitutes what is called the morphogeographic group Criollo, also known as Theobroma cacao L. subsp. cacao. Criollo cacao was thought to originate in Central America and to have evolved independently from the cacao type from the Amazon basin. Morphological diversity and recent molecular analysis had supported this hypothesis. Cacao populations from the Amazon basin are included in the second morphogeographic group, which is called Forastero and is considered as a different subspecies (sphaerocarpum). In order to gain a better understanding of the origin and the genetic basis of the cacao type cultivated in Central America, a study was carried out, after rigorous sampling, using RFLP and microsatellite markers. In contradiction to previous studies, "wild" and domesticated cacao from Central America was found to be genetically close and closer to Colombian-Ecuadorian individuals than Colombian-Ecuadorian individuals were to Peruvian ones. RFLP and microsatellite analyses also revealed a high level of homozygosity and a significantly low genetic diversity within the Criollo group. The results therefore suggest that the Criollo group probably originated from a few individuals in South America and that humans participated in spreading these individuals in Central America.