Fermentation of Theobroma cacao L. seeds has been considered to be the most important factor influencing cocoa flavour and has accordingly received most attention. Development of a test procedure in which small amounts of wet cocoa seeds in net bags are inserted in fermentations of wet seeds from single or mixed genotypes has allowed the flavour potential of a wide range of genotypes to be examined. Flavour profiles of cocoa liquors from genotypes grown at BAL Plantations Sdn Bhd, Malaysia differed consistently for various replicate preparations indicating a strong genetic contribution to flavour. In the present study, similar flavour profiles were developed from cocoa from the same genotypes grown in Brazil and Malaysia and subjected to the same conditions of post-harvest processing. Genetic fingerprinting by Rapid Amplified Polymorphic DNA (RAPD) analysis confirmed that most of the genotypes tested for flavour in Brazil and Malaysia were the same, although there were also a few erroneous identifications. The results confirmed the contribution of genotype to cocoa flavour. There appeared to be a minor effect of environment on cocoa flavour development. Mis-identification of genotypes might be more common than is currently realized, and represent a problem for transferring results between various research programmes.