Theobroma cacao L., the chocolate tree, is an important tropical tree-crop that provides sustainable economic and environmental benefits to some of the poorest and most ecologically sensitive areas of the world. Ceratocystis wilt (CW), caused by the fungus Ceratocystis cacaofunesta, is a highly dangerous disease capable of killing the cacao plant. Histopathological studies of the host–pathogen interaction are an effective resource to study pathogenesis which will ultimately lead to a better elucidation of the mechanisms of host resistance. We analyzed the development of C. cacaofunesta reproductive structures, the pattern of fungal colonization and the anatomical responses of cacao resistant (TSH 1188) and susceptible (CCN 51) genotypes to CW. Results showed that conidia germination started within 4 h after inoculation (hai) in agar, by 12 hai conidia germination was 80 %. The resistant genotype showed little or no fungal colonization compared to the susceptible genotype. Host reactions were characterized by greater quantities of gels, gums and tyloses in the susceptible genotypes compared to the resistant. The susceptible genotype had a large number of cells surrounding the xylem vessels that were infused with dark brown phenolic compounds. The host defense reaction observed near the xylem in the resistant genotype, suggest that a mechanism involved with resistance to C. cacaofunesta.