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The rapid ongoing changes in the Central Arctic Ocean call for baseline information on the pelagic fauna. However, sampling for motile organisms which easily escape vertically towed nets is challenging. Here, we report the species composition and catch weight of pelagic fishes and larger zooplankton from 12 trawl hauls conducted in ice covered waters in the Central Arctic Ocean beyond the continental slopes in late summer. Combined trawl catches with acoustics data revealed low amounts of fish and zooplankton from the advective influenced slope region in the Nansen Basin in the south to the ice-covered deep Amundsen Basin in the north. Both arctic and subarctic-boreal species, including the ones considered as Atlantic expatriate species were found all the way to 87.5o N. We found three fish species (Boreogadus saida, Benthosema glaciale and Reinhardtius hippoglossoides), but the catch was limited to only seven individuals. Euphausiids, amphipods and gelatinous zooplankton dominated the catch weight in the Nansen Basin in the mesopelagic communities. Euphausiids were almost absent in the Amundsen Basin with copepods, amphipods, chaetognaths and gelatinous zooplankton dominating. We postulate asymmetric conditions in the pelagic ecosystems of the western and eastern Eurasian Basin caused by ice and ocean circulation regimes.