Krill and pteropods play a key role in polar ecosystems, as they provide a large amount of food for larger organisms, linking phytoplankton to higher trophic levels. Despite their important role, little is known about the genetic structure and genetic patterns of these organisms in the Arctic and Southern Ocean. As polar pelagic ecosystems are undergoing drastic changes, it is important to get a more precise knowledge about spatial genetic structures of krill and pteropods, of which several species are impacted by the consequences of environmental changes. This study therefore focuses on krill and pteropod species belonging to the bipolar genera Thysanoessa, Limacina and Clione. Phylogeographic patterns were explored by examining their genetic structure with the mitochondrial gene CO1. Samples of the different species were taken at different locations in the Southern Ocean (Antarctic Polar Frontal Zone, Weddell Sea, Antarctic Peninsula region) and in the Arctic (Fram Strait, Greenland Shelf), and compared with existing sequences from public databases. Genetic patterns of Thysanoessa inermis from the Arctic Ocean were compared to those of Thysanoessa macrura from the Southern Ocean. Due to their high pelagic dispersal capacity, a genetic homogeneity was expected, which is higher within swarms than between. A more pronounced genetic heterogeneity, linked to geographic populations and distinct water masses, was expected for the two pteropod genera, including the Arctic Limacina helicina helicina and Clione limacina limacina and Antarctic Limacina helicina antarctica and Clione limacina antarctica. The observed patterns were compared between regions and genera.