Phylogenetic analysis of a fragment of the mitochondrial genome and qualitative and quantitative assessments of morphological variation suggest that, in its current conception, Thylamys pusillus (Desmarest, 1804) is a complex of at least three species. In the taxonomic arrangement proposed in this work, the populations in the Argentinean provinces of Entre Rios and Corrientes are here referred to T citellus (Thomas, 1912), while the small Thylamys that lives in the Argentinean Dry Chaco are provisionally referred to T. pulchellus (Cabrera, 1934). In our scheme, Thylamys pusillus is restricted to the Bolivian and Paraguayan Chaco and the vicinities of northern Formosa province in Argentina. We provide emended diagnosis for T. citellus and T. pulchellus, together with detailed morphological descriptions and discuss their distinctiveness from other species of Thylamys. In addition, we included new distributional data.