A new Africa-wide framework for the analysis of fresh and brackish water fish distributions, AfriBasins, is presented. River and lake basins and subbasins are delimited in a standardised way, based on the HydroBasins dataset. To illustrate its potential, this framework is used to analyse the distribution of fish species within the Congo basin. Four large clusters could be recognised: the Upper Congo basin and the closely associated Kasai drainage, which together form the southern Congo basin cluster that shows some affinities with southern Africa; the Lower Congo basin cluster, characterised by many marine and brackish species in its lower part and a largely endemic fauna further upstream; the northern and north-eastern Congo basin cluster, including the Middle Congo River main channel and its right bank tributaries upstream from and including the Ubangi; and the central left bank affluents of the Middle Congo and the north-western Congo basin cluster, with the Sangha showing affinities with the neighbouring Lower Guinean ichthyofaunal province.