The selection of fine flavour cocoa and coffee varieties can lead to attractive niche markets but germplasm need to be analysed for non-volatile compounds and aroma precursors. In the present study, green beans of 202 Theobroma cacao L. accessions (acc.), 64 Coffea arabica L. acc., 35 C. canephora Pierre ex A. Froehner, 7 C. arabusta Capot & Aké Assi and 2 C. canephora × C. congensis A. Froehner hybrids cultivated in Santo, Vanuatu, and harvested at full maturity, were analysed using High Performance Thin Layer Chromatography (HPTLC). In cocoa, 11 compounds were quantified: two alkaloids, two catechins, five proanthocyanidins, and two anthocyanins. Multivariate analyses revealed that Amenolado acc. are differentiated from Criollo, Forastero and Trinitario acc. due to their low caffeine, catechins, and proanthocyanidins contents. Hybrids involving an Amenolado parent also produce low non-volatile compounds contents. In coffee, 11 compounds were quantified: sucrose, two alkaloids, and eight chlorogenic acids. The two major species were differentiated by their mean caffeine content (12.69 mg/g in C. arabica vs. 16.04 mg/g in C. canephora), which is highly correlated with CGA and other chlorogenic acids. Each of the eight chlorogenic acids presented higher values in C. canephora. The ratio sucrose/alkaloids + chlorogenic acids was significantly higher in C. arabica (3.24) than in C. canephora (1.68) which could be an explanation for its comparative sweetness. Coffea arabusta interspecific hybrids presented an intermediate value (2.64). Congusta hybrids were low in sucrose. HPTLC is a cost-efficient technique when applied to germplasm characterization of non-volatile compounds in green cocoa and coffee beans. Chemotype selection appears promising for the development of fine flavor varieties.