Carletonomys cailoi was discovered in 1998 in a silt deposit in San Cayetano Partido, southeastern Buenos Aires Province.
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It was initially referred to the genus Noronhomys, which is currently known only from the island of Fernando de Noronha off northeastern Brazil, but in 2008 Argentinean mammalogist Ulyses Pardiñas established it as the holotype of a new genus and species of rodent in a publication in the Journal of Mammalogy.