The first species of Transandinomys to be scientifically described was T. talamancae, named as Oryzomys talamancae by
Joel A Allen in 1891. Several other species were soon added to the genus Oryzomys, then more broadly defined than currently, that are now classified in Transandinomys, including Oryzomys bolivaris (now Transandinomys bolivaris) by Allen in 1901. In his 1918 review of North American Oryzomys, Edward Alphonso Goldman placed Oryzomys talamancae and Oryzomys bombycinus (=T. bolivaris) each in their own group, but thought them closely related. In 1960, O. talamancae was synonymized with "Oryzomys capito" (=Hylaeamys megacephalus), but it has again been recognized as a separate species since 1983. The species was reviewed by Guy Musser and Marina Williams in 1985 and again by Musser and colleagues in 1998, who documented the diagnostic characters of the species, its synonyms, and its distribution. The 1998 study by Musser and colleagues also documented Oryzomys bolivaris as the correct name for the species previously known as Oryzomys bombycinus and reviewed that species.
In 2006, Marcelo Weksler published a broad phylogenetic analysis of Oryzomyini, the tribe to which Oryzomys and related genera belong, using morphological data and DNA sequences from the IRBP gene. O. talamancae appeared within "clade B", together with other species formerly associated with Oryzomys capito. Some analyses placed it closest to species now placed in Euryoryzomys or Nephelomys, but with low support. O. bolivaris was not included. Species of Oryzomys included in Weksler's study did not cluster together in his results, but instead appeared dispersed across Oryzomyini, indicating that the genus was polyphyletic and should be split up. Later in the same year, Weksler, Alexandre Percequillo, and Robert Voss introduced ten new genera of Oryzomyini formerly placed in Oryzomys, including Transandinomys for Oryzomys talamancae and O. bolivaris, with the former as the type species. Transandinomys is now one of about thirty genera within Oryzomyini, a diverse group of well over a hundred species. Oryzomyini is one of several tribes within the subfamily Sigmodontinae of the family Cricetidae, which includes hundreds of other species of mainly small rodents, distributed chiefly in Eurasia and the Americas.