During the 18th century, the information available on non-European plants and animals was often incomplete, distorted or missing. Although European paintings of that period depicted South American camelids as long-necked, giraffe-like animals with horns, or resembling camels, deer or dogs, Linnaeus described the alpaca very accurately as Camelus pacos ("Camelus peruvianus laniger Pacos dictus"), placing it alongside the llama Camelus lama ("Camelus peruvianus Glama dictus"), the dromedary Camelus dromedarius and the Bactrian camel Camelus bactrianus in the genus Camelus. Charles Linnaeus did not include the wild South American camelids in his classification because the guanaco and the vicuña were only described years later when P.L.S. Müller described the guanaco as Camelus guanicoe in 1776 and J.I. Molina described the vicuña as Camelus vicugna in 1782.
The llama, alpaca, guanaco, vicuña, camel and dromedary were classified in the same genus (Camelus) until 1805. Thereafter, the first four were classified within the genus Lama. In 1924, Miller separated the vicuña from the other South American camelids, creating the genus Vicugna. This classification indicated that the alpaca, llama and guanaco were part of a group where the guanaco would be the ancestral species, while the vicuña was separated as a wild species that was never domesticated. Many scientists did not accept the creation of Vicugna, and continued to classify the vicuña in the genus Lama.
Although it has always been accepted that the guanaco is the ancestor of the llama, over the years there have been a number of hypotheses regarding the origins of the alpaca. The oldest hypothesis was that the alpaca descended from the vicuña and the llama descended from the guanaco and was supported by Darwin and others. The second hypothesis, and the most widespread, held that the alpaca and the llama descended from the guanaco and that the vicuña was never domesticated.
This debate has only been resolved thanks to the advancement of science with the tools provided by DNA analysis that have made it possible to resolve the evolutionary history of these species. The complete genome sequencing of the four species makes it clear that the alpaca is the domestic form of the vicuña and the llama is the domestic form of the guanaco.