The video that was collected in November and December 2015 during horizontal transects with the PELAGIOS towed camera system during cruise MSM49 in waters around Cabo Verde in the eastern tropical north Atlantic was annotated using the video and annotation reference system (VARS) developed by the Monterey Bay Aquarium Research Institute. In total more than 40 hours of video were collected and annotated, and 43 taxonomic groups were annotated, mostly consisting of gelatinous zooplankton. This resulted in a dataset of diversity and abundance data from which vertical distribution, abundance and diversity of pelagic fauna could be derived (https://doi.pangaea.de/10.1594/PANGAEA.919333). This dataset provides examples of images of annotated organisms.