Endophytic Trichoderma inoculated into roots have been known to colonize above ground tissues of cacao. In this study, we evaluated Trichoderma asperellum spread and impact on endophytic fungi occurring naturally in leaf, stem and root tissues after application through foliar spraying, stem infusion, and soil drenching into cacao seedling of two, four, and five months old respectively. This fungus was isolated from all plant tissues, although by stem infusion was not detected in leaf tissues, and regulated different co-occurring fungal endophytes influenced by seedling age. Dominant endophytes detected were  Fusarium 1 and 3 in seedlings used for foliar spraying, morphospecies 1 and 3, and Lasiodiplodia 1 in seedlings used for stem infusion, and Lasiodiplodia 2, 3 and 4, and Paecilomyces in seedlings used for soil drenching. In general, these dominant fungi were more numerous in tissues of the control than in those inoculated with T. asperellum over three weeks post inoculation, but instead four weeks post inoculation. The pattern changed in tissues following soil drenching where higher colonization of dominant fungi in treated seedlings began earlier. These data showed that T. asperellum can deploy systemically, through the application of foliar spraying, infusion, and soil drenching, to almost all parts of the cacao plant even in the presence of endogenous fungal endophytes and the last fungi their self can reach high colonization in the presence of T. Asperellum. Therefore, this presence together of introduced and co-occurrence of endophyte fungi could potentially be used to develop a method for suppressing cacao pathogens.