A new species of the murid rodent genus Thomasomys is described from the Cordillera Oriental of eastern Ecuador, a major range of the northern Andes that remains almost completely unexplored mammalogically. In order to provide a baseline for future faunal inventory work in these mountains, this report summarizes specimen data from the vicinity of Papallacta (0°22′S, 78°08′W), a small village located near tree line on the eastern (Amazonian) slope. In addition to the new Thomasomys, the local fauna includes 32 other species of nonvolant mammals, of which several (Akodon latebricola, Thomasomys cinnameus, and T. erro) have not been reported since their original descriptions in the 1920s. Taxonomic research based on this material indicates that at least six taxa currently treated as synonyms or subspecies should be recognized as valid species, including Thomasomys popayanus (possibly including T. nicefori) and T. praetor (both formerly synonymized with T. aureus), T. cinnameus and T. hudsoni (both formerly synonymized with T. gracilis), T. erro (formerly synonymized with T. cinereiventer), and Coendou quichua (formerly synonymized with C. bicolor). Although the Papallacta fauna includes several clades (“genera”) that extend to south- and north-temperate latitudes, over half of the local species are endemic to the northern Andes (north of the Huancabamba Deflection in northern Peru); among these northern-Andean endemics, three species known only from northeastern Ecuador provide evidence for a distinct center of endemism in the Cordillera Oriental. Quantitative estimates of species-level faunal complementarity indicate substantial horizontal turnover (between ecologically similar highland sites) on the scale of a few hundred kilometers, and almost complete vertical turnover (between adjacent highland and lowland sites) on the scale of about 2000 m. Both phenomena pose significant challenges for timely inventory work across vast Andean landscapes that remain sparsely sampled by mammalogists. In particular, the middle elevations of the eastern slope of the northern Andes, a densely forested region approximately 2 km high and over 1500 km long, remain a mammalogical terra incognita.