The Arctic is experiencing climate change-related warming at a faster rate than any other region. This is inducing unprecedented reductions in sea ice cover, increasing freshwater inflow and rising ocean temperatures. These environmental changes are already having drastic impacts on the marine ecosystem; affecting species composition, distribution and food web structure in the Arctic Ocean. Pelagic Themisto amphipods are an important link between secondary producers and marine vertebrates at higher trophic levels. Two co-existing species dominate the Arctic region: Themisto libellula, considered a genuine Arctic species and Themisto abyssorum, considered a sub-Arctic, boreal species. Both prey on mesoplankton but are thought to occupy different niches. T. libellula is larger, feeds on herbivorous copepods and is a key prey item for seabirds, key Arctic fish species and certain marine mammals. Whereas T. abyssorum is smaller, feeds on omnivorous and carnivorous zooplankton and is considered an indicator species of warmer water masses. Both species have exhibited recent changes in abundance and range shifts, likely as a result of the Atlantification of the Arctic. Many aspects of the ecology and genetic structure of these two species are not well studied, despite their importance in the food web and biogeochemical cycles. Further understanding of the phylogeography and distributional patterns of these key zooplankton species is crucial to understanding how they will be affected by climate change and how this will impact the ecosystem. This study focuses on the genetic structure and connectivity of both Themisto species as well as their association with Arctic and Atlantic water masses. We do this by analysing and comparing mitochondrial cytochrome oxidase I gene sequences according to the geographic populations. These data reveal a contrasting genetic structure, predicting T. libellula will be less able to cope with environmental changes than T. abyssorum. Distributional data of both species and their abundances are statistically analysed in relation to hydrographic data. Individuals were collected between 2016 and 2020 on a number of international campaigns, from a broad geographic distribution including Svalbard fjord systems, the Fram Strait and Southern Greenland.