While there is still an enormous amount of work to be done simply to get a decent inventory of the African fresh and brackish water fish diversity, new projects, new sampling strategies and new methodologies are slowly improving our level of understanding. However, contemporary studies not only solve long-standing problems but also uncover new challenges. Since several years, the ichthyology unit of the Royal Museum for Central Africa, Tervuren, in collaboration with local partners, is undertaking a number of initiatives to boost the studies on the poorly known Central African ichthyofauna, and especially the Congo basin. These are combined with intensive collecting efforts in various regions such as the Lower Congo, the Inkisi, the Léfini, the region around Kisangani, the Ituri, Lake Tanganyika, the Malagarazi, the Luapula and the Lualaba. Hence, a much more fine-grained geographic coverage is now available for many fish taxa. A large collaborative framework with Belgian partners and the University of Kisangani resulted in two major multidisciplinary expeditions in the Central Congo basin in 2009 and 2010, and the creation of a new biodiversity centre at Kisangani in order to assure the sustainability of the collecting and research initiatives. The combination of major sampling efforts and detailed morphometric studies (classical and geomorphometric) eventually combined with genetics, lead to some remarkable results. While some groups remain remarkably stable after revision, others are completely overhauled. The family Hepsetidae is a case in point. For many decades regarded as a monogeneric and monospecific family, a thorough review revealed that there are actually six clearly distinct species of African pike. In depth studies on various groups revealed geographic variation that was often found to render species delineation difficult. Another challenge is represented by the discovery of complex evolutionary histories in some Cichlids, Cyprinids and Mastacembelids, indicating that hybridization may be more common than previously thought.