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One of the most striking components of the modern assemblage of South American mammals is the semiaquatic capybara (Caviidae, Hydrochoerinae), the biggest rodent in the world. The large hydrochoerines are recorded from the middle Miocene to the present, mainly in high latitudes of South America. Although less known, they are also recorded in low latitudes of South America, and in Central and North America. We report the first record of capybaras from the late Pliocene of Colombia, found in deposits of the Ware Formation, Guajira Peninsula in northeastern Colombia. We analyze the phylogenetic position within Caviidae, the possible environmental changes in the Guajira Peninsula, and the implications of this finding for the understanding of the Great American Biotic Interchange. The morphological and phylogenetic analyses indicate that the hydrochoerine of the Guajira Peninsula is a new species, ?Hydrochoeropsis wayuu, and this genus is most closely related to Phugatherium. According to the latest phylogenetic results, this clade is the sister group of the lineage of the recent capybaras (Neochoerus and Hydrochoerus). ?Hydrochoeropsis wayuu is the northernmost South American Pliocene hydrochoerine record and the nearest to the Panamanian bridge. The presence of this hydrochoerine, together with the fluvio-deltaic environment of the Ware Formation, suggests that during the late Pliocene, the environment that dominated the Guajira Peninsula was more humid and with permanent water bodies, in contrast with its modern desert habitats.