Molecular study of mitochondrial and nuclear genes and cytogenetic analysis were performed to examine possible patterns of speciation in the diverse Lophuromys flavopunctatus species complex of Ethiopia. Phylogenetic analysis of mtDNA data resulted in an unresolved bush of ten deeply diverged haplotype groups corresponding to potential species either well supported by various types of character or ‘cryptic’. The cytogenetic analysis showed represen- tatives of five of these mtDNA lineages to share an identical karyotype (2n = 70, NFa = 84), that has not been found previously in Ethiopia. One of them, L. cf. sikapusi, being a member of the L. flavopunctatus species complex, dem- onstrates remarkable morphological similarity to representatives of another species complex, L. sikapusi s.l., which might be considered as a result of convergent evolution in analogous environments. Analysis of RAPD data suggests that at least two mtDNA types might have been subject to interspecific transfer due to hybridization. In the case of two sympatric haplotypes of L. brunneus we may assume that the contemporary pattern of variation between them can be explained by relatively recent hybridization with another distinct species, L. flavopunctatus. The formation of two groups belonging to distinct mitochondrial lineages within northern populations could be associated with more complex processes including ancient hybridization.