The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics. Genomics use cases for improving public health surveillance in Africa Pathogen genomics has the potential to transform public health surveillance by improving outbreak detection and investigation, tracking transmission routes and networks, monitoring genetic changes that impact pathogenicity, diagnostics, therapeutics, and vaccines, and assessing the effectiveness of policies and interventions. 13 Recommended and well established genomics use cases WHO guidance for global surveillance of HIV drug resistance, 21 tuberculosis drug resistance, 22 malaria, 23 antimicrobial resistance, 24 vaccine-preventable diseases, 25 and food borne pathogens 26 already recommend or