The origins of South America's domestic alpaca and llama remain controversial due to hybridization, near extirpation during the Spanish conquest and di¤culties in archaeological interpretation. Traditionally, the ancestry of both forms is attributed to the guanaco, while the vicu·a is assumed never to have been domesticated. Recent research has, however, linked the alpaca to the vicu·a, dating domestication to 6000^7000 years before present in the Peruvian Andes. Here, we examine in detail the genetic relationships between the South American camelids in order to determine the origins of the domestic forms, using mitochondrial (mt) and microsatellite DNA. MtDNA analysis places 80% of llama and alpaca sequences in the guanaco lineage, with those possessing vicu·a mtDNA being nearly all alpaca or alpaca^vicu·a hybrids. We also examined four microsatellites in wild known-provenance vicu·a and guanaco, including two loci with non-overlapping allele size ranges in the wild species. In contrast to the mtDNA, these markers show high genetic similarity between alpaca and vicu·a, and between llama and guanaco, although bidirectional hybridization is also revealed. Finally, combined marker analysis on a subset of samples con¢rms the microsatellite interpretation and suggests that the alpaca is descended from the vicu·a, and should be reclassi¢ed as Vicugna pacos. This result has major implications for the future management of wild and domestic camelids in South America.