Before searching for individuals resistant to pod rot disease caused by various species of the genus Phytophthora, it is essential to study pathogen diversity. Good knowledge of that diversity provides a clearer understanding of the diversity of attacks, notably of "host x pathogen" interactions that might sometimes complicate the search for resistance. This chapter therefore proposes a review of the genetic diversity of cocoa tree Phytophthora pathogens. This genetic diversity is investigated using various recently developed molecular tools. Following an introduction to the different cocoa tree pathogen species, the diversity of the moste widespread species will be examined.