We collected optical datasets during horizontal video transects with the Pelagic In Situ Observation System (PELAGIOS), a towed camera system, deployed at different localities in the Fram Strait during the R/V Polarstern expedition PS126 from May to June 2021. This system allowed to collect video footage of the larger-sized pelagic fauna (macro- and megazooplankton) in the water column at 3 stations, at depths ranging from 20 m to 2000m. Gelatinous zooplankton taxa, including ctenophores, cnidarian medusae and siphonophores, were annotated and identified to the lowest taxonomic level possible (species, genus). In this dataset, we present the annotations of these video transects with the associated metadata, and for each annotation, a 4-second videoclip. The name of each video file contains the following information: Observation ID, Expedition, Station, Taxa, Depth (example 1_PS126_HG4_Aglantha_digitale_400.mp4). This dataset was used to assess diversity, distributions and abundance data on gelatinous zooplankton in the rapidly changing Atlantic-Arctic gateway, Fram Strait.