The archaeological record indicates that guanacos inhabited the Patagonia ofChile and Argentina about 13,600 years ago, but were unable to migratefurther south owing to the presence of glacial and water barriers thatcovered much of southern South America including the island of Tierra delFuego. As environmental and ecological conditions improved, guanacos, alongwith other large mammals including horses, colonized the area. As a resultof continued world-wide glacial melting, ocean levels rose and Tierra delFuego became isolated from the mainland approximately 8000 yearsago. Although island populations generally exhibit lower levels of geneticvariation than their counterpart mainland populations, it is difficult topredict how much less variation island populations will exhibit. An analysisof mitochondrial cytochrome b and ATPase-8 sequences and 15 nuclearmicrosatellite loci revealed that both populations retained appreciablegenetic diversity. The island population, however, exhibited much lessvariation than the mainland population. Measures of genetic variationrevealed modest, but significant genetic differentiation, consistent withseparation of the two populations approximately 8000 years ago. Theassessment of levels of genetic diversity and population differentiationamong populations of the wild South American camelids is becomingincreasingly important as interest mounts in their utilization as arenewable resource.