Theobroma grandiflorum (Willd. ex Spreng.) Schum. is a tree originating in the Amazon forest. In Brazil, it is known as cupuassu and, like Theobroma cacao, belongs to the family of the Malvaceae. The pulp is used by the food industry and the seeds, which are rich in fatty acids, are used in cosmetics. As for cacao, cupuassu cultivation is affected by the witches’ broom disease (WBD), caused by Moniliophthora perniciosa (M. perniciosa). Despite its economical value, cupuassu culture lacks genetic information, compromising its plant breeding program development. The aim of this research was to increase molecular knowledge about WBD resistance. The progeny of 168 individuals obtained by crossing two contrasting cupuassu clones (174 and 1074, resistant and susceptible to WBD, respectively) were evaluated. The first consensus genetic map consisting of 1438 markers was produced using genotyping by sequencing (GBS) and genome sequencing of the neighboring species T. cacao (Criollo B97) as reference. The analysis of synteny between T. cacao and T. grandiflorum showed that the average homology between the linkage groups of the two species was 97.2%. A resistance quantitative trait locus (QTL) was identified on chromosome 6 of resistant parent 174 at marker 6M1252980. The phenotypic data associated with that QTL corresponded to observations after natural and artificial infection with M. perniciosa. The biological process associated with this QTL may play a role in resistance and susceptibility to M. perniciosa.