Cacao (Theobroma cacao L.) is among the most important cash crops in tropical countries. The existing cacao genetic diversity represents a key resource to ensure the long-term sustainability of cacao cultivation but it remains vastly underused. The objective of this paper is to describe the current state of conservation and use of cacao genetic materials in six countries in South (Peru and Ecuador) and Central America (Nicaragua, Honduras, El Salvador, Guatemala). For each country, we reviewed the regulations for cacao genetic resources, we carried out a survey of 176 gene banks and nurseries, and we performed a review of breeding and selection programs. We found that all countries had poor systems of certification, verification and traceability. Gene banks conserved many local materials in Peru and Ecuador while they mainly conserved international clones in Central American countries. In all countries except Honduras, more than half of the gene banks did not have any characterization or evaluation data of the conserved materials. Although nurseries in all countries had fair productive capacities, varieties sold were unevenly characterized in Peru, Ecuador and Guatemala, and less than half of the nurseries provided technical assistance to farmers in Ecuador and El Salvador. Breeding and selection programs had not fully used the cacao diversity in these countries. Based on the results, we identified the strengths and weakness, as well as the most appropriate investment areas for each country. A better conservation and use of cacao genetic resources in Latin America would benefit not only these countries but also the whole cacao sector.