The biogeography of Iceland is controversial. Some authors believe that all Icelandic life originated after postglacial dispersal events (tabula rasa hypothesis), but others assume that some organisms survived the last glaciation in ice-free refugia. To extend existing knowledge of the freshwater biogeography of Iceland, we used a snail species, Radix balthica, as a model system. Based on a sample of 1,070 sequences of the cytochrome c oxidase subunit I gene from Iceland and from islands of the British Isles and continental Europe, a distinct Icelandic lineage was discovered. To explain the origin of the Icelandic lineage, two alternative scenarios were proposed: (i) postglacial colonization followed by rapid divergence under an elevated mutation rate and (ii) ancient preglacial colonization with survival during multiple glacial events in geothermal refugia and slow divergence under a ‘standard’ mutation rate. The results of neutrality tests and mismatch analyses and the star-like shape of the network indicated a recent population expansion of this species in Iceland. The modeling results within an approximate Bayesian computation framework supported the tabula rasa scenario. Based on our findings, a Holocene origin for the Icelandic lineage of R. balthica was suggested, which evolved under a mean rate of 7.95 × 10⁻⁷ substitutions/site/year.