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We investigated the population genetic structure and phylogenetic relationships of four morphospecies of Semisulcospira sampled from multiple South Korean drainages. One, S. extensa, displayed modest levels of genetic diversity and formed a species-specific clade for both mitochondrial (mt) and nuclear markers. In contrast, the other three, S. coreana, S. gottschei, and S. libertina, were polyphyletic for both mt and nuclear markers. They formed, together with other nominal congeners (S. forticosta, S. multicincta, S. nodiperda, and S. tegulata), a taxonomically heterogeneous species complex containing population-level admixtures of genotypes from numerically predominant modal clades in addition to rare, phylogenetically divergent, mt and nuclear genotypes. The modal mt haplotypes exhibited far more geographic than taxonomic congruence and typically co-clustered into drainage-specific tip clades, irrespective of nominal taxonomic status. The evolutionary origins of the observed non-extensa phylogenetic heterogeneity are unclear at present although the available data do not support paralogous mt marker phenomena or the presence of cryptic species. We cannot distinguish among retention of ancestral polymorphisms or recticulate evolutionary origins as explanatory mechanisms and it may require the genetic characterization of Semisulcospira lineages throughout much of their collective east Asian range to address this issue. Based on the available data, we consider it best to view all of our non-extensa Korean study taxa as a single polymorphic species complex of the type species S. libertina. There is considerable evidence that similarly complex genetic structuring, at least for mt, may be typical of many other freshwater cerithioidean snail taxa. In light of our Semisulcospira results, we suggest that meaningful molecular phylogenetic characterization of freshwater cerithioidean lineages may require the use of both mt and nuclear markers together with population level sampling of all nominal taxa within regional drainages.