This research was conducted with the objective of characterizing morphologically the endophytic fungi associated with native cocoa to assess their antagonistic ability to control Moniliophthora perniciosa. It was developed in the laboratory of Plant Pathology of Instituto de Cultivos Tropicales(ICT), located in the district of Banda Shilicayo, province and department of San Martin. For the morphological characterization was used 68 isolates of endophytic fungi from Alto Amazonas. Variables and categories were employed to determine the genetic distance with 185 markers, which was calculated using the DICE coefficient (Dice, 1945). Cluster analysis was done using the algorithm UPGMA (Unweighted Pair-Group Method Arithmetic Average usingn) using the Darwin program (Dissimilarity Analysis and Representation for Windows). To evaluate the antagonistic capacity of fungal endophytes, were carrie...