The human microbiome is now known to play important roles in health and disease, but while microbiome research on European and North American populations has increased exponentially, African populations may be underrepresented. The relative lack of data could impair medical progress for Africans and obscure important treatment targets. To characterize the knowledge gaps, researchers recently searched the literature for next-generation sequencing studies published through April 1, 2020, that included African samples. Thirty-three out of 54 African countries were represented in the 168 studies found, primarily South Africa, Kenya, and Uganda. Only 26.8% of studies focused on diseases of significant public health concern in Africa. Among studies with intercontinental collaboration, the USA was the most common collaborator, and the first and last authors of most studies were not affiliated with African institutions. In addition, the primary funders were American or European institutions. Although the results of the studies were not analyzed, this systematic review identifies significant gaps in microbiome research in Africa and emphasizes the need for local leadership, capacity expansion, intra-continental collaboration, and local government investment in microbiome research within Africa.