ABSTRACT The genus Aspergillus has been isolated from cocoa plantations worldwide. However, there is not enough information about its role in the occurrence of diseases. Aspergillus niger strains were characterized by morphological and molecular techniques. The sequences of A. niger were deposited in the GenBank databases. In addition, the antagonistic effect of Trichoderma asperellum VSL80 against A. niger strains was evaluated, obtaining a biocontrol index (BCI) between 15.36 and 88.71%. Scanning electron microscopy showed that the Trichoderma hyphae grew in parallel with the hyphae of A. niger and, in some cases, they were found together with the hyphae of the pathogenic fungus preventing their development. On the other hand, the maximum enzymatic activity of xylanases produced by A. niger in submerged culture was 1.128 U mL1 at 96 h. The morphological and molecular characterization of A. niger strains confirms its presence in Mexico. In addition, information obtained of the BCI may be important for the development of strategies for the prevention and control of this fungus. The enzymatic activity of A. niger during mycoparasitism by T. asperellum could explain the low BCI observed in some A. niger strains confronted with T. asperellum. Finally, the xylanolytic enzyme production by A. niger indicated that this fungus could be used in the industry to obtain xylanases.