Cocoa tree (Theobroma cacao L.) is cultivated mainly in tropical regions and produces beans that are used for chocolate manufacture. Worldwide, cocoa bean production is threatened by biotic stresses, mainly fungus, oomycetes, virus and other pests. The understanding of the determinism of the plant-pathogen interactions as well as the different and integrated ways to manage the cocoa diseases at field level began the focus of several research groups. Here, we did an overview of the several cocoa diseases, of the traditional breeding methods as well as the molecular assisted ones recently developed, of the molecular and omics resources currently available, and of the new biotechnology approaches—including genome edition and nanotechnologies—that are used at basic and applied research levels. We also described the main germplasm and collections worldwide as well as the use of the cocoa diversity as main source of disease resistance.