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The Congo basin is the second largest basin of the world after the Amazon. With an estimated 1250 valid species and hundreds to be described, it is also the second fish species richest basin in the world after the Amazon. Nevertheless, its ichthyofauna is still poorly studied. The last decade, several studies have been undertaken to explore the ichthyofauna of parts of the basin, which has led to a significant increase of the number of documented species in the areas explored, and the description of several new species. The present study focusses on the most important north-eastern affluents of the Middle Congo apart from the huge Ubangi system: the Itimbiri, Aruwimi and Lindi/Tshopo. About 8000 fish specimens sampled during five recent expeditions to the region have been identified, and about 2000 relevant specimens in the existing collections have been examined.In a first step, an inventory was made of the ichthyofauna of the region. A total of 317 species belonging to 28 families were listed: 231 from the Itimbiri, 244 from the Aruwimi, and 184 from the Lindi/Tshopo. The family of the elephant fish, Momryridae, was the most species rich in all three basins. For the Itimbiri and Aruwimi, recent expeditions were mainly executed in parts of the basins that were poorly represented in the museum collections. These expeditions provided several additional species records: 47 from the Itimbiri (20.5% of the total diversity in this basin) and 69 from the Aruwimi (28.4 %). This illustrates the importance of additional surveys, especially to different parts of river basins, to cover as much as possible of the total ichthyodiversity.Previous to the tectonic uplifting of the East African Rift System, the north-eastern tributaries were connected with the Nile system via a paleo-lake. Therefore we assessed the impact of this ancient connection on the distribution of the modern ichthyofauna. However, little similarity in ichthyofauna was found between the two systems in the study region. The few common species found, were all widespread over larger parts of Africa, or their identification was found to be based on doubtful records, or it were taxa with an uncertain taxonomic status.The Aruwimi basin harbours numerous waterfalls and rapids that could form barriers for fish dispersal. As such, this basin provides an interesting study area to examine fish distribution patterns. Clear differences in species richness and composition have been found between the headwaters (the Ituri River) and the lower reaches. The headwaters harboured few species with the Cyprinidae as most dominant family, while the lower reaches harboured far more species with the Mormyridae as the most dominant family. Waterfalls on the Epulu (an important right-bank affluent of the Ituri), and on the Ituri itself most probably contributed to the very low species richness in the headwaters. Nevertheless, their impact on the ichthyofauna was rather small since the species composition in the Epulu and other parts of the Ituri was generally similar.In addition to physical barriers, environmental conditions (abiotic factors) also had a significant influence on the fish community structure. Again, the results illustrated important differences between the Aruwimi headwaters and the lower reaches, with the colder, higher altitude headwaters having a higher pH and conductivity. Also differences between the lower reaches of the three basins were found, with e.g. lower oxygen levels in the Itimbiri.DNA barcoding was applied as a complementary tool to disentangle the diversity in the region. The identification success was low compared to other barcoding studies, as a result of many discrepancies between morphology-based species identifications and the different lineages recognized by this molecular technique. Two or three genetic lineages were found within each of ten out of 160 species from which we had more than one sample, indicating the possible presence of cryptic species. Conversely, in four cases, two morphologically distinct species clustered into the same genetic lineage, which could be due to introgression after hybridization. The DNA barcodes confirmed the existence of previously known identification problems within certain genera such as Enteromius, Clarias and Labeo, but also confirmed species delineations, which were uncertain based on morphology, in Bryconaethiops and Distichodus. DNA barcoding also illustrated the hypothesis that the waterfall on the Epulu has a certain influence on the fish distribution, since haplotypes of seven out of 14 species were slightly different between specimens of the Epulu and Ituri.During the identification process, plentiful taxonomic problems were encountered. Five cases were tackled more into detail.A first case was the morphological review of the African pike Hepsetus within the Congo basin. This review was the last in a series comprising the complete revision of the genus, which used to be considered as monospecific. Three species could be distinguished in the Congo basin: H. cuvieri, H. lineata and H. microlepis, the latter being revalidated in the presented study.A second case is the description of a new Brycinus species from the Epulu River: B. sp. "epuluensis". The specimens were initially identified as B. imberi, but differed from the latter mainly due to the presence of only 6 premaxillary teeth (vs. 8) and a broad dark mid-lateral band. A third case concerned a population of 'Haplochromis' specimens in the Ituri River. It was the first time this genus was recorded from the region, and the specimens were clearly different from all known species of the Congo basin. Its yellow colouration was however reminiscent of that of ‘H’. aeneocolor from Lake George (Nile system), and specimens from the Ituri have been morphologically compared with the type series of this species. Only small differences could be found in a few measurements; these were postulated to be the result of adaptations to the riverine conditions in the Ituri. The species has most probably been accidently introduced in the Ituri in the framework of aquaculture.In a fourth case, the diversity in Labeobarbus species of the Epulu River has been examined based on morphology and genetics (mtDNA, cytb). This led to the delineation of at least four species in the region, but also the detection of several specimens (ca. 10% of the specimens examined) that were considered putative hybrids. The recognition of hybridization within this taxonomic group is in line with previous studies, and a comparable complex encountered in the Inkisi (Lower Congo).For the last case, a combined morphometric and DNA barcoding approach was applied to assess the diversity of Enteromius in the study region, and in some more detail the E. miolepis/eutaenia complex throughout the Congo basin. Literature-based identifications assigned all specimens to four different species, but the barcoding results revealed no less than 23 separate lineages within these four 'a priori' species. Morphometric analyses confirmed that most of these lineages also differed in morphology and could be considered as separate species, which would mean that the species diversity within this genus of small Cyprinids is currently severely underestimated.Clearly there is still much left to be explored and discovered in the extensive Congo basin. This is testified by two striking outcomes of this dissertation. Firstly, there is the exceptional high diversity detected in the genus Enteromius, which could point to unique speciation events in riverine conditions, that have not yet been reported for any other taxon within the Congo basin or in African freshwaters for that matter. Secondly, we discovered complex hybridization patterns within Labeobarbus, again unreported in any other genus, the underlying mechanisms of which also still need to be unraveled. These examples illustrate that the merits of biodiversity studies can go way beyond just serving as a vital basis for further biological studies.