Phytophthora megakarya is an important pathogen of cocoa in Africa. We used isozyme and RAPD markers to estimate the genetic diversity and structuring among 161 isolates, from the known distribution area of the fungus which corresponds to the cocoa belt in Ghana, Togo, Nigeria, Cameroon, Gabon and Sao Tome. Thirty six and 44 multilocus patterns were identified with isozymes and RAPDs, respectively. Patterns were separated into two highly differentiated genetic groups with both types of markers, one located in Central Africa and the other in West Africa. This distribution coincides with two major biogeographical domains which may reflect an ancient evolution of P. megakarya in this part of Africa. The genotypic diversity was lower in West Africa as compared to Central Africa. Inside Central Africa, isolates from Gabon and Sao Tome were highly differentiated based on RAPDs. Four intermediate marker patterns corresponding to isolates sampled near the border between Nigeria and Cameroon were putatively derived from genetic exchanges between the two major groups. The mating type determination permitted to confirm the high prevalence of A1 over A2. Although clonal multiplication seems to be the rule, indices of other reproduction means have been detected.