The 32 cacao clones selected as being resistant following the witches' broom epidemic and for having distinct productivity were characterized according to their genetic diversity and were submitted to a new selection. These plants were assessed for eight years at the Oceania Farm (FO) in Itagibá, Bahia, Brazil. The 13 microsatellite primers generated an average of 11.7 amplicons per locus, and based on them it was demonstrated that the 32 clones distribute themselves in groups apart from the nine clones used as controls. The 32 materials displayed significant differences in relation to the characters assessed in the field. Two criteria were formed from the classification of the most productive and resistant plants, and then used to select plants within the clusters. The selected plants displayed potential for the cacao improvement program, that they have a high production and high resistance to witches' broom.