Lama guanicoe (Müller, 1776) is one of the most important South American large mammal species for both biologists, ecologists and archaeologists, and body size of modern and prehistoric populations of guanaco has been one of the most studied parameters. In this paper, we evaluate the latitudinal differences in body size of different modern populations of guanaco from Argentinean Patagonia based on osteometric data of their long bones. The osteological sample is made of 110 fully-fused individuals drawn from three different guanaco populations from continental and insular Patagonia covering the latitudinal interval from S40° to S54.5°. Quantitative data for the four long bones selected are analyzed with univariate and multivariate parametric statistical techniques. Apparently consistent with Bergmann's rule, results show that guanaco specimens from S53–54.5° are bigger on average than those from S48–52° which are, in turn, bigger than those from S40°. We observe a high and significant covariation between different environmental variables (maximum temperature, net primary production, and winter precipitation) and body size of the guanaco populations. Nevertheless, when the temporal factor is incorporated into the analysis of this geographical gradient of body size the scenario becomes more complex. We conclude that the current clinal pattern observed in Patagonia is the result of several microevolutionary and biogeographic processes related to an adjustment of body size to different environmental and ecological drivers and to the consequences of isolation in Tierra del Fuego that occurred around the Pleistocene-Holocene transition.