The recent COVID-19 pandemic has accentuated the profound impact that widespread epidemics exert on global health and societal dynamics. Rather than being an isolated incident, it is part of a continuum of outbreaks that have shaped human history. Pathogens such as M. leprae, M. tuberculosis, and Y. pestis, alongside viruses such as Hepatitis and Variola virus have been identified in ancient remains, indicating their long-standing impact and far-reaching effects on population movements. Besides harbouring the greatest genetic diversity in the world, the African continent is home to a broad spectrum of lifestyles, ranging from hunting and gathering, pastoralism and farming. The specific interactions between lifeways, health and adaptation to their environment provide a unique framework for studying the effects of pathogen exposure across populations. While it has been argued that epidemics could have played a role in the decline and eventual collapse of populations and civilizations in Africa, direct evidence for this remains elusive. Despite its vast potential, sub-Saharan Africa has seen limited exploration in the comprehensive analysis of ancient DNA (aDNA) for pathogen detection. This project aims to combine microbial metagenome data with endogenous genomic data obtained from aDNA sequencing from human remains. The systematic study of aDNA from a wide array of archaeological contexts holds the potential to elucidate the effects infectious diseases have had on ancient populations in Africa, and the ways in which pathogens have shaped demographic and societal continuity. Additionally, by analysing ancient DNA from skeletal remains, we can detect and uncover pathogens that may have caused previously undocumented epidemics, gain insights into the factors that contribute to their virulence and infectivity and trace the patterns of genetic variation in pathogens over time.Finally, by analysing pathogen aDNA, we have the unique opportunity to track the evolution of pathogens over time by comparing ancient and modern strains.