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The first known specimen was obtained by W.G. Palmer in 1904[6] and the next year, Oldfield Thomas of the British Museum of Natural History described this animal as the holotype of a new species he named Nectomys dimidiatus.[2] He placed it in the genus Nectomys, commenting that it was much smaller than but otherwise similar to previously known members of that genus.[2] The species was listed as a Nectomys in taxonomic overviews in the next decades, including a 1944 review of the genus by Philip Hershkovitz.[7]

After examining the holotype in London, Hershkovitz instead placed the species in the genus Oryzomys in 1948. He remarked that it was an especially distinctive member of that genus, and hence classified it in its own subgenus Micronectomys.[8] J. Hernández-Camacho described a second species of Micronectomys, Oryzomys (Micronectomys) borreroi, from Colombia in 1957.[9] In 1970, Hershkovitz treated O. dimidiatus in another publication and conceded that his name Micronectomys was a nomen nudum ("naked name") because he had not explicitly mentioned characters differentiating it from other taxa in his 1948 publication.[10] Nevertheless, he did not do anything to rectify the situation, and Micronectomys remains a nomen nudum.[11] Hershkovitz also noted that while O. dimidiatus resembles a juvenile Nectomys in external anatomy, it is otherwise similar to the marsh rice rat (Oryzomys palustris).[10] He accepted O. borreroi as an Oryzomys, but did not think it closely related to O. dimidiatus.[9] Six years later, Alfred Gardner and James Patton instead suggested that O. borreroi was a Zygodontomys, and in his 1991 review of that genus Robert Voss confirmed that it is the same as Zygodontomys brunneus.[12]

A second specimen was obtained in 1966 and the find was published in 1971 by Hugh Genoways and Knox Jones, who noted that the species is closely similar to O. palustris.[13] Later workers affirmed the relationship between O. dimidiatus, O. palustris and associated species like O. couesi.[14] Fiona Reid reported in 1997 that a third specimen had been found.[15] In 2006, Marcelo Weksler and coworkers removed most of the species formerly placed in Oryzomys from the genus, because they are not closely related to the type species O. palustris, but kept O. dimidiatus as an Oryzomys.[14]

Oryzomys dimidiatus is now recognized as one of eight species in the genus Oryzomys.[16] O. dimidiatus is further part of the O. couesi section, which is centered around the widespread Central American O. couesi and also includes six other species with more limited and peripheral distributions.[17] O. couesi occurs with O. dimidiatus in southeastern Nicaragua.[18] Many aspects of the systematics of the O. couesi section remain unclear and it is likely that the current classification underestimates the true diversity of the group.[19] Oryzomys is classified in the tribe Oryzomyini ("rice rats"), a diverse assemblage of American rodents of over a hundred species,[20] and on higher taxonomic levels in the subfamily Sigmodontinae of family Cricetidae, along with hundreds of other species of mainly small rodents.[21]