On the basis of integrated analyses of karyologic, molecular and morphologic data of Wiedomys samples distributed throughout north-eastern Brazil, we suggest the existence of more than one evolutionary lineage within the genus and describe a new species apparently restricted to western Bahia state, in the Cerrado morphoclimatic domain. This new taxon differs from W. pyrrhorhinus by narrower incisive foramina, smaller molar rows, presence of an alisphenoid strut, and diploid number of 60 chromosomes. Phylogenetic analyses of cytochrome b sequences of this new species and samples of W. pyrrhorhinus from the Caatinga of Bahia state, depict the two taxa as reciprocally monophyletic clades separated by 14.7–15.6 % corrected genetic distance. This new species and W. pyrrhorhinus are allopatric, the former occurring in the Cerrado morphoclimatic domain and the latter endemic of the Brazilian semi arid Caatinga.