This dataset features the geographic location of Lama guanicoe by subspecies across Chile. Coordinate system: UTM 19South WGS84 Lineages are from: Marin JC, González B a, Poulin E, Casey CS, Johnson WE (2013) The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America. Mol Ecol 22: 463–482. Available: http://dx.doi.org/10.1111/mec.12111