Theobroma cacao is currently under serious threat due to various diseases, of which Phytophthora pod rot, commonly called 'black pod' is one of the most economically important. Four fungal species of the same genus are primarily responsible for this disease: P. palmivora, P. megakarya, P. capsici and P. citrophthora. Among these, P. palmivora is the most common, being present in most cacao producing countries. P. palmivora can cause yield losses of 20-30% and tree mortality of 10% annually. P. megakarya occurs only in West African countries, but is the most virulent among the four species. In Africa it causes 30-90% annual crop losses and thus it poses a severe threat to the cacao industry and to producers in Africa. Both in vitro pod husk inoculation assays and in planta pod inoculation assays verified that P. megakarya was more aggressive. Studies suggest effective early penetration by P. megakarya makes it a more destructive pathogen. Since the Phytophthora species that cause disease on cacao differ so much in their virulence, we developed specific primers for QPCR identification of each species. At the same time we characterized the genetic diversity of P. palmivora and P. megakarya in Ghana, a major producer. Through further genetic analysis, we estimate the genome size of P. megakarya to be 116.9 Mb and the P. palmivora genome size to be 100 Mb. P. palmivora appears to be tetraploid whereas P. megakarya, despite its larger genome, is not. Comparative genome analysis between these two species shows that both species carry large numbers of plant-pathogen interaction proteins including the RxLR effectors. An in-depth comparative analysis of genomics and transcriptomics between these two closely related species is being carried out to highlight the molecular mechanism behind their virulence and support the development of effective control measures. This is critical since Phytophthora spp. in general and P. megakarya specifically, represent a significant threat to