One of the main challenges to adequately conserve the African fish fauna is to improve our so far unsatisfactory taxonomic knowledge of important portions of the ichthyofauna. In the present study, we attempted to unravel the taxonomic diversity of some species of Enteromius Cope, 1867, a problematic African fish genus, recently collected in the north-eastern part of the Congo basin. We used an integrative approach, combining DNA barcodes and morphological analyses. For one of the species complexes found, the E. miolepis/eutaenia species complex, we evaluated taxonomic diversity over a larger geographic scale within the Congo drainage system. Although initial literature-based species identifications allowed us to assign all examined specimens to four tentative species, DNA barcodes indicated the presence of 23 distinct mitochondrial lineages. The majority of these lineages appeared endemic to particular rivers, and in most rivers multiple lineages occur in sympatry. Subsequent exploratory morphometric analyses indicated that almost all these lineages are morphologically distinguishable and that they may therefore represent undescribed species. As only a part of the Congo basin and a subset of the species diversity within Enteromius were examined, it appears that the species richness of Enteromius in the Congo basin is severely underestimated.