The area of the northern East African rift-valley lakes Kivu, Edward and Albert (KEA) is a hotspot of terrestrial biodiversity. For fishes, it is one of the most enigmatic regions in terms of biogeography as it is situated at the intersection of three major ichthyo-geographic provinces (Nilo-Sudan, East Coast and Congo), and as it featured a turbulent tectonic history. Although the region is much poorer in species than the neighbouring basins, it has high levels of species endemicity, especially for lacustrine cichlids. It was speculated that the region, and especially the three deep-water lakes, acted as a refuge during recent climatic changes, such as the dry periods that led to the desiccation of Lake Victoria (ca. 15 000 years ago). In the KEAFish project, we will test this by studying the entire ichthyofauna of the region using classical taxonomy, standard sequencing methods, and state-of-the-art genomic techniques. This will allow us to characterise how the region’s fish fauna emerged, and how it shaped or influenced the current fish faunas of the rest of the continent.