Rapid warming in the Arctic is drastically impacting marine ecosystems; affecting species composition, distribution and food web structure. Themisto amphipods are a key link between secondary producers and marine vertebrates at higher trophic levels. Two co-existing species dominate in the region: Themisto libellula, considered an Arctic species and Themisto abyssorum, a sub-Arctic, boreal species. T. libellula is larger, feeds on herbivorous copepods and is crucial prey for seabirds, key fish species and marine mammals. Whereas T. abyssorum is smaller, feeds on carnivorous zooplankton and is considered an indicator of warmer water masses. Both species have already exhibited changes in abundance and range shifts, likely due to 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 phylogeography and distributional patterns 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, from Svalbard fjord systems, the Fram Strait and Southern Greenland. Distributional data are statistically analysed in relation to hydrographic data. These data reveal a contrasting genetic structure, predicting T. libellula will be less able to cope with environmental changes than T. abyssorum.