Nacional is a variety of cocoa tree known for its "Arriba" aroma characterised mainly by fruity, floral, and spicy aromatic notes. In this study, the genetic basis of the fruity aroma of modern Nacional cocoa was investigated. GWAS studies have been conducted on biochemical and sensorial fruity traits and allowed to identify a large number of association zones. These areas are linked to both the volatile compounds known to provide fruity flavours and present in the beans before and after roasting, and to the fruity notes detected by sensorial analysis. Five main metabolic pathways were identified as involved in the fruity traits of the Nacional population: the protein degradation pathway, the sugar degradation pathway, the fatty acid degradation pathway, the monoterpene pathway, and the L-phenylalanine pathway. Candidate genes involved in the biosynthetic pathways of volatile compounds identified in association areas were detected for a large number of associations.