Societal Impact Statement Recent surveys conducted on Amazonian cocoa trees in their home range are a unique opportunity to assess the aromas, diversity and potential of the Ecuadorian Amazon to create new aromatic cocoa varieties. Our results reveal informations about the diversity and genesis of aromas in Ecuadorian fine cocoa. The great aromatic diversity could enrich cocoa flavour selection programmes and provide Amazonian populations with new income linked to aromatic varieties, which could lead to a 'grand cru' chocolate. Until now, breeding programmes have been mainly focused on improving characteristics for production, but in recent years cocoa quality has been increasingly examined to meet market expectations. Ecuador is known worldwide for its fine or flavour cocoa from the Nacional variety. Currently, farmers mainly grow the modern Nacional variety of cocoa trees (hybrids between the ancestral Nacional and Trinitario) while the ancestral Nacional variety tends to be neglected. In order to enlarge the genetic resources related to this ancestral variety, several surveys were carried out in its area of origin located in the South Ecuadorian Amazonia. The 202 trees resulting from these surveys were genotyped using GBS (Genotyping By Sequencing) markers and their dried-fermented beans were characterised for both their aromatic volatile compounds and sensorial quality. A genome wide association study (GWAS) was carried out with the aim to study the genetic and biochemical bases of the aroma traits of this population and to better exploit them in breeding programmes. Some association areas and candidate genes related to spicy and woody aromas were found for the first time in Theobroma cacao. Some association areas and candidate genes related to floral and fruity aromas common to other studies were identified. Our results support the hypothesis that aroma formation may be related to a defence reaction to biotic and abiotic stresses generated by the fermentation process.