In order to determine the level of genetic diversity of cultivated banana trees and to define the best conservation strategies, the genetic diversity of dessert and plantain banana trees was studied using microsatellite markers. The phylogenetic tree obtained from genetic dissimilarity indices revealed a heterogeneity of groups formed from vernacular names. Most of the names attributed to plantain in the Mono-Couffo department refer to the same variety except for the names ‘Adjangan ayawe, Adjangan ayvlan and Mandangan dekpo’ which were found to be different and probably refer to different varieties. For dessert bananas similar cases have also been observed. However, identical vernacular names found in different areas or in the same area were found to be genetically different.