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Understanding the nature and dynamics of Africa's collaborative research networks is critical for building and integrating the African innovation system. This paper investigates the collaborative structure of the African research systems, with focus on regions and integration. Drawing on a bibliometric analysis of co-authorship of African research publications in 2005---2009, we propose an empirically derived grouping of African research community into three distinct research regions: Southern---Eastern, Western, and Northern. The three regions are established and defined in terms of active co-authorship clusters within Africa, as well as through co-authorship links with non-African countries and regions. We examine co-authorship links both at the national and city levels in order to provide a robust and nuanced empirical basis for the three African research regions. The collaboration patterns uncovered cast light on the emerging innovation systems in Africa by pointing out the differing national, regional, and global roles of countries and cities within collaborative research networks. Lack of research capabilities is the primary factor arresting the development of African innovation systems, but our analysis also suggests that Africa's internal research collaboration suffers from structural weaknesses and uneven integration. We also identify that South Africa, and some emerging new research hubs, hold critical networking function for linking African researchers.