The first species of Transandinomys to be scientifically described was T. talamancae, named as Oryzomys talamancae by Joel Asaph Allen in 1891 [REF].
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.