Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal was mediated by humans. The latter scenario predicts low levels of genetic differentiation across a species’ range, coupled with a genetic signature of recent range expansion. Location: Southeast Asia, the Philippines, Wallacea and the south-western Pacific. Methods: We analysed sequences of mitochondrial DNA from 204 samples collected throughout the range of this species. We use phylogenetic and popu- lation genetic methods to distinguish between predicted geographical patterns of genetic variation that might indicate natural or human-mediated dispersal. Results: In contrast to predictions derived from similar studies of taxonomy and natural history, we found L. smaragdina to be characterized by highly structured and seemingly geographically stable mitochondrial gene lineages. Main conclusions: Our results demonstrate a novel pattern of widespread species distribution, never before observed in vertebrates of the Indo-Australian Archipelago. Although this widespread and highly dispersive species is capable of long-distance dispersal, and has a clear history of over-water dispersal, it exhibits sharp genetic differentiation across its range. Our results suggest that random waif dispersal has been a pervasive ongoing phenomenon throughout the evolutionary history of this species.