During the Lower and Middle Miocene times, a rather homogenous ichthyofauna probably extended on the African continent, north to the Central African Shear Zone. This ichthyological continuum has been assumed to correspond to an ecological continuum. Combined modifications in the topography (e.g., Neogene plumes) and in the environment (e.g., desertification and Saharan extension) limited its distribution to the current Nilo-Sudanese province, but also affected the ichthyological composition of each basin within the province. Outside the Eastern Rift area, only Chad yielded a fossil record along in the Late Miocene and the Pliocene. Today, the fish specific diversity is lower in Chad than in certain other Nilo-Sudanese basins. Here we present the current knowledge on these Late Neogene change in diversity and discuss the interest of the fossil record to understand the processes of extinction and diversification that shape the modern diversity in intertropical Africa.