A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge ofTheobroma cacaoL. pathogens’ molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies ofT. cacaoeukaryotic pathogens, focusing on the plant–pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author’s affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera wereMoniliophthora(105 studies),Phytophthora(59 studies) andCeratocystis(13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common inT. cacaopathogen genomes. This review contributes to the knowledge aboutT. cacaodiseases, providing an integrated discussion ofT. cacaopathogens’ molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.