We studied the taxonomy, distribution, and ecology of species within Praomys, a common rodent genus present in rainforests and montane forests in sub-Saharan Africa. The taxonomy of the group is problematic, and for the sampled region of Kisangani (Democratic Republic of Congo) no prior genetic study has been published. We used a combination of molecular (cyt b sequencing) and craniometric techniques (canonical analyses of skull measurements) for the species identification of a total of 654 specimens. We confirm the presence of Praomys minor in the region, up to now only known from the type and paratype specimens. At least seven species are present in the Kisangani region, and two clades occur along both banks of the Congo River. The present-day distribution of the genus seems to be influenced by large-scale rainforest fragmentation related to drier periods in geological history. The Congo River could in this case constitute a modern barrier to gene flow when the climate enabled rainforest expansion. The tributaries of the Congo River play no role in limiting Praomys species distribution, apart from the Aruwimi River for Praomys jacksoni s.l.