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cies 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 Rob

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