Qualitative, mensural, genetic, and phylogenetic analyses were conducted to clarify species limits, distributions, and relationships in the poorly known Amazonian rodent genus Scolomys. Scolomys melanops is characterized by consistent differences in comparison with all other samples of the genus. However, our data do not support the recognition of S.juruaense as a valid species, but rather as a synonym of S.ucayalensis. Only minimal differences in Cyt-b sequences were present between S.juruaense and S.ucayalensis, and phylogenetic analyses consistently retrieved a monophyletic genus Scolomys with the relationship ((S.juruaense+ S.ucayalensis) + S.melanops). The apparent morphological distinctiveness of S.juruaense in the original description was due to small sample sizes and comparisons of adult specimens from Brazil with the juvenal type material of S.ucayalensis from Peru. The two species that we recognize, S.melanops and S.ucayalensis, can be separated by the short, relatively wide rostrum and wide zygomatic arches of S.melanops versus the longer, relatively thinner rostrum and absolutely narrower zygomatic arches of S.ucayalensis. Scolomys melanops ranges from the eastern slopes of the Andes in Ecuador to near Iquitos in Amazonian Peru, and we document the presence of S.ucayalensis in western Brazil, northern Peru, and southern Colombia.