A new species of the cricetid rodent genus Thomasomys is described from the montane forests of the Cordilleras del Cóndor and Kutukú, southeastern Ecuador, at elevations between 1,770 and 2,215 m. The species has a large body size (head and body length 137–147 mm) in comparison with other species in the genus, and also is distinguished from its congeners by presenting a tail longer than the head–body length, presence of genal vibrissae 1 and 2, wide presphenoid, first and second lower molars with ectolophid, and third lower molar slightly shorter than the second. A molecular phylogeny based on mitochondrial genes resolved the new species a member of the “aureus” group, most closely related to Thomasomys aureus sensu stricto (genetic distance 8.57%) and as well as an additional undescribed species from southeastern Ecuador. This finding increases the diversity of Thomasomys to 46 species, of which 17 species are present in Ecuador. In addition, the species described herein is the first Thomasomys from the Amazonian basin, a genus that up to now was thought to be restricted to Andean ranges.