Agromorphological diversity structure of the elite shea trees identified in village lands and conserved in situ in the districts of Bagoué and Tchologo by the shea breeding program of the University of Peleforo Gon Coulibaly (UPGC, Côte d'Ivoire), are not known. In the present study, we characterized the agromorphological parameters of 220 elite shea trees using a set of 12 quantitative traits. The results showed that elite shea trees population has been structured into three morphological clusters or genetic pools that do not overlap with the original geographic areas. Morphological Cluster I contain elite shea trees with small trunk diameters carrying large leaves and producing fewer fruits per tree. Morphological Cluster II consisted of elite shea trees with stronger trunks bearing small leaves and producing a high number of fruits per tree. Morphological Cluster III regrouped elite shea trees of medium trunk diameters carrying medium sized leaves; fruit production level is intermediate compare to preceding groups. The elite shea trees of morphological Clusters II, which are more interesting from an agronomic point of view, can be used as grafting trees for the production of high-yielding grafted plants for farmers in Côte d'Ivoire.