Diseases associated withPhytophthoracause considerable losses in cocoa production worldwide. Analyzing genes, proteins, and metabolites involved inTheobroma cacao’s interaction withPhytophthoraspecies is essential to explaining the molecular aspects of plant defense. Through a systematic literature review, this study aims to identify reports of genes, proteins, metabolites, morphological characteristics, and molecular and physiological processes ofT. cacaoinvolved in its interaction with species ofPhytophthora. After the searches, 35 papers were selected for the data extraction stage, according to pre-established inclusion and exclusion criteria. In these studies, 657 genes and 32 metabolites, among other elements (molecules and molecular processes), were found to be involved in the interaction. The integration of this information resulted in the following conclusions: the expression patterns of pattern recognition receptors (PRRs) and a possible gene-to-gene interaction participate in cocoa resistance toPhytophthoraspp.; the expression pattern of genes that encode pathogenesis-related (PRs) proteins is different between resistant and susceptible genotypes; phenolic compounds play an important role in preformed defenses; and proline accumulation may be involved in cell wall integrity. Only one proteomics study ofT. cacao-Phytophthoraspp. was found, and some genes proposed via QTL analysis were confirmed in transcriptomic studies.