Gelatinous zooplankton are known to play an important role in World Ocean ecosystems. As climate change continues to cause profound environmental shifts in Fram Strait, a key transitional zone between the North-Atlantic and the Arctic Ocean, the lack of understanding of how gelatinous zooplankton are affected by these environmental changes creates a significant gap in knowledge about the future state of Arctic ecosystems. In this study, we used in situ observations obtained by the towed underwater camera system PELAGIOS (Pelagic In situ Observation System) to establish one of the first regional baselines of large gelatinous zooplankton diversity and abundance in mesopelagic and bathypelagic zones. Our data included 16 taxa of gelatinous zooplankton, with the most abundant being from the family Rhopalonematidae (Aglantha digitale and Sminthea arctica) and the suborders Physonectae and Calycophorae. We used a joint species distribution modelling approach to better understand their three-dimensional distribution patterns and assess the environmental drivers of gelatinous community structures. The most significant drivers were temperature and depth. Spatial distribution modelling based on in situ measurements revealed that the highest abundance and diversity of jellyfish are expected at the edges of the West Spitsbergen and East Greenland current systems. The near-future projections indicate that with continued temperature increase, the gelatinous zooplankton community in the Fram Strait will become less diverse but more abundant. Among taxa of the Rhopalonematidae family, we expect the abundance of Aglantha digitale to increase by 2% throughout the water column, while Sminthea arctica will experience a loss of up to 60% by 2050.