Multimammate mice of the genus Mastomys are widespread in sub-Saharan Africa and occur in a wide range of open habitats. Representatives of this genus are the most common African rodents, the main vertebrate agricultural pests and vectors of human pathogens. In Ethiopia, the biogeographically most complex eastern African country, several species have been reported, but their distribution has never been described because of their cryptic morphology. Here we present genetically identified species from 377 Ethiopian Mastomys specimens and analyse their distributional patterns. The genus, represented by four species, inhabits most of the country, with the exception of the highest mountains and dry areas, such as the Afar triangle and the Somali region. For the first time we document M. kollmannspergeri from a single locality in the northernmost part of Ethiopia. Three previously recorded species are more widespread – M. erythroleucus was found at 32 localities, M. natalensis at 13 localities and the Ethiopian endemic species M. awashensis at 18 localities. and Phylogenetic analysis of mitochondrial cytochrome b gene sequences indicates that only one of the six phylogroups of M. natalensis and one of the four phylogroups of M. erythroleucus are represented in Ethiopia. Haplotype network analysis indicates two subclades of Ethiopian M. erythroleucus separated by the Ethiopian Rift Valley. Using presence records, we constructed distribution models for the species and analysed the level of overlap. The predicted distribution shows most overlap between M. awashensis and M. natalensis, which is in agreement with empirical data as both species were found in sympatry at four localities. A medium level of overlap was predicted between M. natalensis and M. erythroleucus and both species were found co-existing at two localities. This study not only presents the first detailed distribution of cryptic Mastomys species, but also clearly identifies multimammate mice as model taxa for future evolutionary studies (e.g. the evolution of coexistence or host-parasite interactions) and indicates the regions suitable for such studies.