During the last years, molecular studies revealed significant population differentiation and cryptic species within various benthic and pelagic marine Antarctic taxa. This is unexpected due to the lack of obvious barriers to gene flow and strong current systems. Using mitochondrial (COI, 16S rDNA) and nuclear (28S rDNA: D2) gene fragments, we tested whether two circum-Antarctic benthic shrimps with planktotrophic larvae, Chorismus antarcticus and Nematocarcinus lanceopes, show patterns of regional differentiation. For both species, the 16S and the 28S fragment were invariant. However, for COI we found 24 different haplotypes for Chorismus antarcticus and 54 for Nematocarcinus lanceopes. No significant differentiation was observed among populations or regions. Furthermore, we found signatures of a population expansion in the late Pleistocene hinting at an impact of large-scale glaciations in particular on the shallow-water shrimp Chorismus antarcticus, supporting a (re)colonization and demographic expansion of this shrimp species in response to climate oscillation.