The proposed age of the striking biogeographic disjunction between the Arctic and southernmost South America varies from more than 65 million to a few thousand years, but no estimates based on explicit models and molecular data are available. Here we address the origin of bipolarity in crowberries (Empetrum), which are heath-forming dwarf shrubs with animal-dispersed fruits. We apply a fossil-calibrated relaxed molecular clock to model sequence evolution in two nuclear low-copy and two plastid DNA regions from 41 individual plants (420 clones for the nuclear regions) representing the entire geographic distribution of crowberries. The plastid region matK and four fossil calibration points were used to infer the ages of the crowberry stem and crown groups. All analyses resolved three major crowberry clades (A-C). Clade A contained sequences from the eastern Canadian pink-fruited crowberry (E. eamesii) as sister to clades B and C, which both contained sequences from the black-fruited northern hemisphere crowberry (E. nigrum). Clade B also contained a subclade with all sequences from the red-fruited southern hemisphere crowberry, which is often referred to as a distinct species, E. rubrum. Its closest relatives were consistently identified as black-fruited plants from northwestern North America. The median time to the most recent common ancestor for northern and southern hemisphere crowberries was estimated to 0.56-0.93 Ma, and 0.26-0.59 Ma for the southern plants only. We conclude that a single dispersal by a bird from northwestern North America to southernmost South America, taking place in the Mid-Pleistocene, is sufficient to explain the disjunction in crowberries.