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Ancient pathogen genomics has redefined how infectious disease histories are reconstructed,revealing unexpected origins, transmission routes and lineage turnovers that are invisible frommodern genomes alone. Yet this perspective remains heavily biased toward Eurasia and theAmericas, leaving Africa, central to human evolution, biodiversity and zoonotic emergence,largely unexplored. In this review, we assess the current state of ancient pathogen research inAfrica and synthesize insights from bacterial, parasitic and viral perspectives. We identify Africaas a pivotal frontier for the field and outline strategic priorities to move from isolated detectionstoward continent-scale reconstructions of past disease landscapes, with direct relevance forunderstanding present-day and future epidemic risk.