African freshwater fishes serve as important biogeographical indicators of geomorphological and hydrological history across the continent. However, research focusing on the phylogeny, biogeography, and diversification of African fishes, particularly in central Africa, is relatively scarce. Here, we evaluate three geological hypotheses regarding the formation of the contemporary Congo basin: 1) the dominance of the Ogooué and Kouilou rivers along the western continental margin during the Cretaceous, 2) an eastward-flowing Congo-Zambezian system forming the Rufiji Delta during the Paleogene, and 3) river basin capture resulting in the formation of the Lower Congo River during the Pliocene. To do this, we reconstructed the phylogeny of featherfin tetras of the genus Bryconaethiops using their mitochondrial genomes, estimated diversification chronology, and detected biogeographic transitions in Central Africa. Analysis included a molecular matrix of complete mitochondrial genomes comprising 13 protein-coding genes totaling 14,869 bp for 36 Bryconaethiops and related alestid taxa. Phylogenetic analyses included maximum likelihood, Bayesian fossil calibration, and parametric biogeographic reconstructions. Support for generic monophyly was evaluated using internal and external anatomy with microcomputed tomography (µCT) and conventional morphometric/meristic analyses. Data from museum specimens provided updated distributional ranges for each Bryconaethiops species. Time-calibrated phylogenetic and biogeographic analyses suggest initial diversification of Bryconaethiops occurred in Lower Guinea during the Oligocene (ca. 25 Ma), followed by transitions to the Nilo-Sudan and Middle Congo regions during the Early Miocene (ca. 19–17 Ma). Three distinct Pleistocene dispersal events to the Lower Congo (ca. 0.7–0.05 Ma) and three to the Upper Congo and Malagarasi of Tanganyika (ca. 1.5–0.1 Ma) were detected. Morphological analysis reveals four generic synapomorphies associated with modification of the upper and lower jaws, dentition, and elongation of dorsal-fin lepidotrichia, in addition to evidence for revalidation of B. mocquardianus (Thominot, 1886) from Atlantic coastal rivers of the eastern Gulf of Guinea.