In the world market of fine cocoa, the variety "Nacional" is the most important in Ecuador. This endemic variety is highly valued because of its taste and floral aroma known as "Arriba flavor". In this study, we identified genes linked to Arriba flavor using RNAseq technology of the transcriptome of Nacional commercial clones, which are the result of a selection of a collection of local landraces. For this purpose, we developed cDNA libraries from self-pollinated beans and harvested 18, 20 and 22 weeks after pollination and the latter after fermentation. The cDNA libraries were sequenced using ILLUMINA Hiseq 3000 and the bioinformatic analysis was carried out using the reference genome Criollo B9761/B2 available in CIRAD. The genetic expression analysis allowed us to identify a set of genes expressed in each of the experimental conditions, before and after fermentation, revealing in all the cases the expressed genes and also a set of genes that have not been annotated in the reference genome. Among the genes involved in the biosynthesis pathway of terpenoides and phenolic components, both pathways previously identified as important for cocoa bean quality, RNAseq analysis made it possible to characterize the expression of each identified gene in the analyzed genotypes before and after fermentation. Interestingly one of the genes linked to the synthesis of linalool, a compound identified as one of the terpenes associated with aroma and reported to be in higher concentrations in the Arriba flavor, was shown to be expressed differently among the analyzed Nacional genotypes. Moreover, the differential expression analysis, realized with a pipeline based on the CUFFLINKS protocol, did not identify differentials associated with these biosynthetic pathways, suggesting the need to complement the study by including other higher contrasting genetic varieties.