Our understanding of the tectonic development of the African continent and the interplay between its geological provinces is hindered by unevenly distributed seismic instrumentation. In order to better understand the continent, we used long-period ambient noise full waveform tomography on data collected from 186 broadband seismic stations throughout Africa and surrounding regions to better image the upper mantle structure. We extracted empirical Green’s functions from ambient seismic noise using a frequency-time normalization method and retrieved coherent signal at periods of 7-340 seconds. We simulated wave propagation through a heterogeneous Earth using a spherical finite-difference approach to obtain synthetic waveforms, measured the misfit as phase delay between the data and synthetics, calculated numerical sensitivity kernels using the scattering integral approach, and iteratively inverted for structure. The resulting images of isotropic, shear wavespeed for the continent reveal segmented, low-velocity upper mantle beneath the highly magmatic northern and eastern sections of the East African Rift System (EARS). In the southern and western sections, high-velocity upper mantle dominates, and distinct, low-velocity anomalies are restricted to regions of current volcanism. At deeper depths, the southern and western EARS transitions to low-velocities. In addition to the EARS, several low-velocity anomalies are scattered through the shallow upper mantle beneath Angola and North Africa, and some of these low-velocity anomalies may be connected to a deeper feature. Distinct upper mantle high-velocity anomalies are imaged throughout the continent and suggest multiple cratonic roots within the Congo region, and possible cratonic roots within the Sahara Metacraton.