We present the results of a palaeogenetic analysis of two Late Pleistocene camelids originating in southern Chile. Our analysis of two mitochondrial DNA fragments (control region and cytochrome b gene) reveals that these specimens do not belong to an extinct taxon, but rather to extant vicuña (Vicugna vicugna), whose modern distribution is restricted to the extreme elevations of the Andes, more than 3500 km to the north of where these specimens originated. Our results also suggest fossil specimens from Patagonia that are currently assigned to the extinct taxon Lama gracilis, may actually belong to V. vicugna, implying a continuous distribution of the latter from the southern tip of South America to the Andes during the Final Pleistocene. The haplotypes of both specimens are not present in modern populations, suggesting a loss of genetic diversity concomitant with the contraction of the vicuña geographical distribution during the Final Pleistocene or early Holocene.