bioRxiv, http://dx.doi.org/10.1101/038406George Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Emil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk Rockett, Domnic Kwiatkowski, Chris Spencer, The Malaria Genomic Epidemiology NetworkUnderstanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa.. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.