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Until now, there has been a single Paraguayan record of climbing rats of the genus Rhipidomys (Tschudi, 1845), and the specimen has not been identified at the species level. Remarkably, this record has been overlooked in recent mammal lists. Field work conducted in Paraguay during and since 2006 has produced the second and third records of Rhipidomys for this country. We conducted an assessment of external and skull morphologic variation, as well as Maximum Parsimony and Bayesian analyses based on DNA sequences, all of which indicate that all three known Paraguayan specimens of Rhipidomys belong to the species Rhipidomys macrurus (Gervais, 1855). In addition, we provide information distinguishing R. macrurus from some of its congeners, as well as new natural history data. There is now a total of 31 sigmodontine species with published Paraguayan records.