The Arctic is warming two times faster than the global mean, and a phenomenon known as the ‘Atlantification of the Arctic’ via the Fram Strait is having growing influences on both biological and physical processes in the region. Changes to community composition and function are already underway and these environmental changes will continue to rapidly alter Arctic ecosystems. Greater understanding of how this impacting local marine biodiversity is crucial for formulating accurate predictions of future Arctic marine ecosystems and management decisions. Gelatinous zooplankton (GZP) is a highly diverse group of taxa, including cnidarians, ctenophores and tunicates. Very little is currently known about GZP ecology, particularly in the Arctic Ocean, and even less about how they are being impacted by climate-related changes. Not only are they often actively left out of zooplankton surveys, but GZP are notoriously difficult to catch in good condition because their fragile bodies are easily destroyed by traditional sampling methods. These challenges contribute to GZP taxa regularly being underestimated in biodiversity, distribution and abundance, which has led to a lack of reliable and comprehensive baseline data available, especially in the Arctic. The aim of this study is to apply non-invasive environmental DNA (eDNA) metabarcoding methods to investigate GZP biodiversity and distribution across the Fram Strait. COI mitochondrial and 18s rRNA amplicons from water and sediment samples will be sequenced with Next Generation Sequencing (NGS) and validated with depth-stratified net-catch data. Net-caught specimens will be barcoded where possible, to complement existing reference databases. Oceanographic data will then be incorporated in order to form a holistic baseline dataset of GZP biodiversity across the region. Such data would be a valuable contribution to future research into the deviations in Arctic GZP biodiversity, community composition and distribution over time, as a result of on-going environmental changes.