Thomasomys cinereus is the type species of Thomasomys, type genus of the sigmodontine tribe Thomasomyini. As currently recognized, Thomasomys includes 48 species, all of which are endemic to humid montane or premontane forests in the tropical Andes. Although it has been suggested that T. cinereus is a species complex, this hypothesis has yet to be critically evaluated. Herein we provide a revision of the species based on a qualitative assessment of external, craniodental, and soft morphological traits; morphometric analyses; a phylogenetic analysis based on cytochrome b gene sequences; species delimitation methods; and first-hand examination of type material. Our analyses of genetic data recovered four distinct clades within T. cinereus, one corresponding to T. cinereus sensu stricto (restricted to the montane forests delimited by the Río Marañón, Río Huancabamba, and Río Tablachaca in Cajamarca department, Peru) and three new species: Thomasomys lojapiuranus, sp. nov., from the montane forests of Piura department, Peru, and Loja province, Ecuador; T. shallqukucha, sp. nov., restricted to the Kañaris montane forests in the Peruvian department of Lambayeque; and T. pagaibambensis, sp. nov., restricted to the montane forests of Pagaibamba in Cajamarca department, Peru. These species can be distinguished by several discrete morphological traits of the skull, dentition, mandible, stomach, palatal rugae, and glans penis. Genetic distances among these taxa range from 5.06%–7.65% at the cytochrome b locus, and delimitation analyses based on cytochrome b sequence data support their recognition as distinct species. Our results suggest the existence of previously unsuspected dispersal barriers in the Andes of northern Peru, and they confirm that the Río Marañón is a formidable barrier that limits the distribution of species of Thomasomys as well as other sigmodontine rodents.