Background: The Mediterranean zone of central Chile (30°to 38°S) is one of the 25 diversity hotspots in the world. However, there are few phylogeographic studies which identify the factors that have influenced population diversification in the fauna of this area. In this study, we investigated the phylogeographic structure of Rhinella arunco, an anuran endemic to Mediterranean Chile, using 160 individuals from 23 localities representative of its entire distribution (32°to 38°S). Results: The haplotype network revealed four haplogroups, three of which overlap geographically and only one of which has an exclusive geographic distribution. An analysis of molecular variance indicated that neither watershed limits nor the main rivers in the current distribution of this species have been important geographic barriers against the dispersion of individuals. Finally, the Geneland analysis showed three population units, one of which concurs with one of the haplogroups found in the haplotype network. Together, these analyses indicated a low level of phylogeographic structure for this species. On the other hand, the highest levels of intrapopulational genetic variation were concentrated in the central part of the distribution (33°to 34°S), which may indicate an effect of Pleistocene glaciations on the genetic diversity of the populations in the extreme south of its range.