 The first three specimens of Thomasomys ucucha were collected in 1903 at Tablón in Pichincha Province, Ecuador, by L. Söderström. It was not found again until Robert S. Voss of the American Museum of Natural History collected a total of forty-three specimens at nearby Papallacta, Napo Province, in 1978 and 1980. Papallacta is in a remote area that is difficult to access, and the mammal fauna of the region remains poorly known. In 2003, he formally described the animal as a new species, Thomasomys ucucha, in a publication in American Museum Novitates in which he also reviewed the mammal fauna of Papallacta. The generic name, Thomasomys, honors English zoologist Oldfield Thomas, who named about 2,900 taxa of mammals, and the specific name, ucucha, is the local Quechua word for "mouse". T. ucucha most closely resembles T. hylophilus, which is found further north in Colombia and Venezuela. Both are members of Thomasomys, a diverse genus that occurs in the northern Andes, from Bolivia to Venezuela. Together with Rhipidomys and a few other, smaller genera, Thomasomys forms the tribe Thomasomyini, which includes over fifty species found in South America and Panama. Thomasomyini in turn is part of the subfamily Sigmodontinae of the family Cricetidae, along with hundreds of other species of mainly small rodents.
