Traditional cocoa plantations in Ecuador are mostly composed of a complex mix of highly variable hybrid progenies, which has greatly reduced the population of native trees of the “Nacional” variety, to such a point that they are considered today as heading for extinction, which is increasingly worrying the international chocolate industry. Some years ago, we used genetic molecular markers to identify trees considered to be relics of the ancient original population of the “Nacional” variety, and some wild cocoa trees in a particular region of the southern Ecuadorian Amazon were identified as highly related to the “Nacional” variety. This paper presents the results of two surveys carried out in the southern Ecuadorian Amazon, in the Zamora-Chinchipe Province, in 2010 and 2013. The objective of these surveys was to search for, identify and rescue cocoa trees that might be the wild ancestors of the “Nacional” variety. In 2010, 83 mother trees were collected (budwood, pods and leaves) and 48 in 2013. They were preserved at the Granja Domono experimental farm, near Macas (Morona-Santiago province) and at the Tropical Experimental station Pichilingue, near Quevedo. The trees collected are currently being characterized for their genetic diversity, using molecular markers, and for the biochemical diversity of their beans.