The Caspian Sea has been a highly dynamic environment throughout the Quaternary and witnessed major oscillations in lake level, which were associated with changes in salinity and habitat availability. Such environmental pressures are considered to drive strong phylogeographic structure in species by forcing populations into suitable refugia. However, little is actually known on the effect of lake level fluctuations in the Caspian Sea on its aquatic biota. We compared the phylogeographic patterns of the aquatic neritid snail genus Theodoxus across the Pontocaspian region with refugial populations in southern Iran. Three gene fragments were used to determine relationships and divergence times between sampled populations in both groups. A dated phylogeny and statistical haplotype networks were generated in conjunction with analyses of molecular variance and calculations of isolation by distance using distance-based redundancy analyses. Extended Bayesian skyline plots were constructed to assess demographic history. Compared to the Iranian populations, we found little phylogeographic structure for the Pontocaspian Theodoxus group, with more recent diversification, homogeneity of haplotypes across the Pontocaspian region and a relatively stable demographic history since the Middle Pleistocene. Our results argue against a strong influence of Caspian Sea low stands on population structure post the early Pleistocene, whereas high stands may have increased the dispersal possibilities and homogenisation of haplotypes across the Pontocaspian region during this time. However, prior to this period a more dramatic low stand in the Caspian Sea around a million years ago may have had caused reduction of Theodoxus diversity to a single lineage in the region. In addition, our results provide new insights into Theodoxus taxonomy and outlooks for regional conservation.