Background. Although the Congo basin is the second largest river basin in the world and it has been considered a biodiversity hotspot for fish, still many parts of this basin remain poorly studied. In this study, we examined the poorly known ichthyofauna of three major north-eastern tributaries of the Congo basin (Itimbiri, Aruwimi and Lindi/Tshopo). A checklist of the ichthyofauna is provided and two synonymies are presented. As such, it contributes to unraveling the poorly known fish diversity in the whole Congo basin. An improved knowledge of the ichthyofauna is a sound baseline for further studies and conservation Material and methods. Fish specimens from five recent expeditions have been identified, and the older collection material from the study area, housed at the Royal Museum for Central Africa and other institutions has been checked and re-identified when necessary. Results. In total, 320 species were recorded, 232 of which from the Itimbiri, 246 from the Aruwimi, and 187 from the Lindi/Tshopo, with the Mormyridae being the most dominant family in all three basins. Micralestes sardina Poll, 1938 is relegated to synonymy with Micralestes humilis Boulenger, 1899, and Enteromius trinotatus (Fowler, 1936) is designated as a replacement name for Enteromius tetraspilus (Pfeffer, 1896). Within the Aruwimi, a clear difference in species richness and composition is apparent between the headwaters (Ituri/Epulu) and the lower reaches near the Congo main stream. The headwaters are characterised by low species richness, with the Cyprinidae being the most dominant family, while the lower reaches are more species rich, with mormyrid species being the most dominant. The presence of two waterfalls on the Ituri/Epulu has a noticeable impact on the fish distribution. Finally, the hypothesis that an ancient connection between the north-eastern part of the Congo basin and the region of the Albertine Rift is still reflected in their present ichthyofauna is not confirmed. Conclusions. This study provides a first checklist of the ichthyofauna in the north-eastern tributaries of the Congo basin, and illustrates the influence of physical barriers on fish diversity and distribution.