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Deep-sea hydrothermal vents and cold seeps are biological hot spots with chemolithotrophic bacterial production sustaining both benthic and pelagic organisms. Although efforts have been made to understand the diversity and function of the bacterial composition of these systems, first-level consumers, pelagic single cell heterotrophic organisms, which represent an important link between bacterial production and higher trophic levels, remain un-described in hydrothermal vents and seeps of the Nordic Seas. Here, we used a molecular biodiversity assay to investigate the impact of water masses and hydrothermal vents on the eukaryotic micro-organisms surrounding two vents systems, Jan Mayen Vent Field and Loki`s Castle, and one cold seep, Hakon Mosby Mud Volcano. The assay generated a total of 482 operational taxonomic units (OTUs) based on a 99 % cut-off value, and the OTUs were grouped according to taxonomic rank. Data analysis using hierarchical clustering and non-metric multidimensional scaling with class as taxonomic entries suggested that water masses followed by depth was the dominant effect on eukaryotic micro-organism diversity. However, in one of the vent systems, Loki`s Castle, the community was different compared to the reference station. Our data suggest that while the total production of vent systems is higher than the surrounding waters, the biodiversity of eukaryotic micro-organisms is more influenced by both water masses and depth.