Chrysosplenium iowense Rydb. (Saxifragaceae) is a southern Canadian boreal forest species with a small number of disjunct populations occurring in the Driftless Area of northeastern Iowa and southeastern Minnesota. This disjunction is attributed to the actions of glacial movement and climate change during the Pleistocene. Populations within each of these distributions may have been isolated for 115 000 years or more and, although levels of genetic divergence between these regions may be significant, there is no morphological or cytological variation associated with this geographic break. We employed inter-simple sequence repeat (ISSR) markers to determine patterns of genetic diversity within 12 populations (six Canadian; six Iowan) of C. iowense and elucidate the routes of post-glacial recolonization for the species. Despite finding relatively high levels of genetic divergence (θII = 0.383, θII = 0.299) between Driftless Area and Canadian populations, there is no conclusive evidence of a speciation event within C. iowense. Analyses show moderate levels of genetic diversity within the species (HT = 0.188), the majority of which is partitioned among individuals within populations (68.18%), which were similar across the northern (HT = 0.234, HT = 0.28) and southern (HT = 0.189) ranges. Finally, the patterns of genetic diversity within C. iowense suggest that the Canadian range was established by migrants originating in now extinct refugial populations that existed outside the Driftless Area. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 815–823.