Monothalamous (single-chambered) foraminifers are a major component of the benthic meiofauna in high latitude regions. Several morphologically similar species are common in the Arctic and Antarctic. However, it is uncertain whether these morphospecies are genetically identical, or whether their accurate identification is compromised by a lack of distinctive morphological features. To determine the relationship between Arctic and Antarctic species, we have compared SSU rDNA sequences of specimens belonging to four morphotaxa: Micrometula, Psammophaga, Gloiogullmia, and one morphospecies Hippocrepinella hirudinea from western Svalbard (Arctic) and McMurdo Sound (Antarctic). Wherever possible, we include in our analyses representatives of these taxa from the deep Arctic and Southern Oceans, as well as from Northern European fjords. We found that in all cases, the bipolar populations were clearly distinct genetically. As expected, Arctic specimens were usually more closely related to those from Northern Europe than to their Antarctic representatives. The deep-sea specimens from Weddell Sea branched as a sister to the McMurdo Sound population, while those from the Arctic Ocean clustered with ones from Norwegian fjords. Our study has revealed a high number of cryptic species within each of the examined genera, and demonstrates the unexplored potential of monothalamous foraminifers for use as a tool to evaluate the origin and biogeography of polar meiofauna.