The native Theobroma cacao L variety from Ecuador, known as Nacional, is famousby its particular floral and fine cocoa flavour called "ARRIBA". It has been subjected, however, to genetic erosion, due principally to successive introductions of foreign germplasm, which have hybridised with the native variety. This hybrid population, which now constitute the modern Nacional variety, gradually replaced the native plantations from the beginning of 20 th century. In order to increse our knowledge on the pattern of dicersity among modern Nacional cacao populations.