A time-calibrated phylogeny, based on nuclear ultraconserved elements and including representatives of all major alestid lineages, strongly supports two distantly related clades within the currently accepted concept of Brycinus. The first, which includes the type species of the genus, B. macrolepidotus (herein Brycinus), and a second, composed of taxa previously referred to as the B. nurse group (herein Brachyalestes), are both resolved as monophyletic. These results provide strong evidence for the restriction of the genus Brycinus to nine species, and for the revalidation of the genus Brachyalestes to accommodate 20 valid species. Within Brachyalestes, a new species from the Lulua River basin, initially misidentified as Brycinus kingsleyae, is described and resolved as sister to the widespread, central Congolese lowland species, Brachyalestes bimaculatus. Within Brachyalestes, a subclade mostly restricted to the Central Congo basin is estimated to have undergone diversification within the last 10 million years, suggesting that Late Neogene riverine reorganization likely influenced their allopatric speciation. The split of the new species, endemic to high elevation tributaries of the Lulua River, from its lowland sister species, Brachyalestes bimaculatus, suggests a Late Miocene/Early Pliocene colonization into the upland river ecosystems of the Katanga plateau in the southwestern Democratic Republic of Congo.