The quality of Ecuadorian cacao is presently threatened by the introduction of hybrid material. An estimation of genetic diversity in Ecuador is required in order to avoid the loss of fine flavored cocoa. Genetic variability amongst 60 Ecuadorian genotypes of Theobroma cacao has been evaluated using molecular and phenotypic markers. The two distance matrices derived from the molecular and phenotypic data were found to be correlated (R-2 = 0.5). Dynamic clustering analyses classified the genotypes in two or three groups depending on the markers used. The genotypes coming from Sebastian Arteaga (SA) and Balao Chico (BCH) plantations appeared related to each other suggesting a common genetic origin. They also may be considered as a distinct group with high RFLP homozygosity. The EETP (Estacion Experimental Tropical Pichilingue of Ecuador) collection was comprised of more variable genotypes possessing variable heterozygosity levels. The low heterozygous genotypes may be genetically related to SA and BCH trees, whereas the higher heterozygous genotypes may have resulted from hybridizations between original Nacional material of Ecuador and genotypes imported from Trinidad at the beginning of the century. Thus genetic introgression may have occurred giving rise to a range of variation between Nacional and hybrid forms.