The quality of Ecuadorian cacao is presently threatenedby the introduction of hybrid material. An estimation ofgenetic diversity in Ecuador is required in order to avoidthe loss of fine flavored cocoa. Genetic variabilityamongst 60 Ecuadorian genotypes of Theobromacacao has been evaluated using molecular andphenotypic markers. The two distance matrices derivedfrom the molecular and phenotypic data were found to becorrelated (R = 0.5). Dynamic clustering analysesclassified the genotypes in two or three groups dependingon the markers used. The genotypes coming fromSebasti{àn Arteaga (SA) and Balao Chico (BCH)plantations appeared related to each other suggesting acommon genetic origin. They also may be considered as adistinct group with high RFLP homozygosity. The EETP(Estací}on Experimental Tropical Pichilingue ofEcuador) collection was comprised of more variablegenotypes possessing variable heterozygosity levels. Thelow heterozygous genotypes may be genetically related toSA and BCH trees, whereas the higher heterozygousgenotypes may have resulted from hybridizations betweenoriginal Nacional material of Ecuador and genotypesimported from Trinidad at the beginning of the century.Thus genetic introgression may have occurred giving riseto a range of variation between Nacional and hybridforms.p>