Understanding the introduction pathways of Phytophthora megakarya in newly established cacao plantations is crucial for improving black pod disease management. This study aimed to identify the sources and dispersal routes of P. megakarya in young cacao plantations in Central Cameroon. Three plantations established in 2006, located in two agro-ecological zones and initially free of primary inoculum, were monitored from the first disease outbreaks in 2009 until 2016. Isolates were collected from infected pods, while additional samples were obtained from soil and nearby river and run-off water using a baiting method. Genetic diversity was assessed using 14 polymorphic SSR markers. Relationships among multilocus genotypes (MLGs) were inferred using an eBURST-based Minimum Spanning Tree analysis. A total of 614 isolates were analysed, including 496 from pods, 106 from soil, and 12 from water. Overall genetic diversity was low, with 47 MLGs identified. Two dominant genotypes, MLG11 and MLG16, were consistently detected throughout the study period and across all sampling sources. Pathogenicity assays showed significant differences among a subset of genotypes, with MLG16 displaying the lowest pathogenicity, whereas savanna-associated genotypes were more aggressive. MLG11 and MLG16 were identified as founder genotypes in each agro-ecological zone. The findings indicate that exogenous inoculum was primarily introduced from neighbouring cacao plantations. However, the detection of P. megakarya in river and run-off water highlights the role of water-mediated dispersal in overcoming physical barriers. These results provide insights into local inoculum dynamics and support the development of improved disease management strategies in cacao-growing systems.
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