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Two cocoa types are predominantly being cultivated in Ecuador, the highly appreciated fine Nacional and the high-yielding and disease-resistant CCN51, classified as bulk. With the introduction of foreign germplasm in Ecuador and the international demand for high-quality Nacional cocoa, the present study aims to characterize and compare the flavor profile of Nacional hybrids (EET103, EET559, EET576 and EET577) and CCN51, and to assess the effect of the genotype. The fermented dried beans were processed into liquor and their sensory properties, volatile composition and odor fingerprint were analyzed by trained panelists, headspace–solid phase microextraction gas chromatography–mass spectrometry (HS–SPME–GC–MS), and GC electronic nose (e-nose), respectively, combined with multivariate statistics. Seventy volatiles were identified and semi-quantified, among them, 16 and 14 volatiles conferring fruity and floral aroma notes, respectively. CCN51 was mainly characterized by undesirable odor-active volatiles, whereas the EET cultivars contained the highest concentration of most fruity and floral volatiles, with differences in between EET cultivars. Sensory data highlighted organoleptic differences between the fine and bulk liquors, i.e. the fruity and acid EET flavor strongly differed from the bitter, astringent and off-flavor attributes of CCN51. Principal component analysis (PCA) discriminated firstly between fine and bulk, and secondly between EET identity. Partial least squares analysis identified possible correlations between sensory attributes and volatile compounds. Besides, e-nose proved its usefulness for rapid assessment of the liquors’ sensory profile. The results provide a foundation for understanding the genotype’s contribution to and the compositional basis of Ecuadorian fine and bulk cocoa flavor.