We investigated developmental changes in the primary mycelium of Crinipellis perniciosa upon its interaction with immature and mature leaves of Theobroma cacao. On nutritive medium, the primary mycelium grew significantly slower in the presence of host tissue than without host tissue. In the absence of the cacao leaves, incomplete phase transition occurred after 5 days, wherein older hyphae progressed to the dikaryotic state and growing tips remained monokaryotic. Phase transition occurred between 3 and 5 days on mature leaves, 10 and 12 days on meristematic leaves, and required 2 weeks on T. cacao callus tissue. The biotrophic mycelia were able to invade immature and mature cacao leaves without open wounds or stomata. Club-shaped hyphal tips and the formation of adhesive structures were induced by cuticle extracts and suggest host recognition. The initial cuticular disintegration at the site of penetration was followed by blister formation and complete digestion of leaves by the primary mycelium. The data suggest specific interactions between host and pathogen that control the onset of the necrotrophic phase of the fungus. The data further indicate that primary mycelium rather than spores can be used to study C. perniciosa pathogenicity.