Climate change proceeding at unprecedented pace is currently redistributing life on Earth. In the Arctic region, climate change is acting more rapidly than elsewhere on this planet, and has dramatically altered sea ice thickness and extent. However, for many Arctic taxa, the distribution ranges and population connectivity have remained undocumented. This is particularly so for Arctic gelatinous zooplankton, of which the diversity, abundances and role in the food web are understudied. The hydromedusa Aglantha digitale is highly abundant in the Arctic Ocean, and characterized by a widespread distribution, ranging from temperate waters to the central Arctic. Its distribution in the water column has been linked to the presence of Atlantic water masses, which renders it a likely candidate to benefit from the ongoing “Atlantification” of the Arctic. Despite its ubiquity and abundance, its genetic diversity remains unknown, and it is unclear whether this species is composed of different geographic lineages throughout its distribution range. To compare the genetic diversity and assess the phylogeography of A. digitale, we collected samples from several recent international cruises. Geographic populations from temperate waters, sub-Arctic Greenland, Svalbard and the central Arctic are compared based on sequences of the mitochondrial cytochrome c oxidase subunit I (COI). A better understanding of the distribution and connectivity will help to predict potential range shifts of A. digitale in an “Atlantified” Arctic.