Climate change proceeding at unprecedented pace is currently redistributing life on Earth. Rapid warming of the upper ocean and the atmosphere have altered sea ice extent and seasonal dynamics in the Arctic and the Southern Ocean, in particular the southwest Atlantic sector. Poleward range expansions of temperate species into the polar oceans have already been noted for various planktonic groups, whereas genuine polar species have been seen to contract their ranges. These shifts have the potential to significantly alter pelagic communities, food web structure and energy flow to higher trophic levels such as seabirds, fish and mammals. For our studies, we focus on two so far neglected key pelagic groups: i) the predatory amphipod genus Themisto and 2) gelatinous zooplankton, including scyphozoans, hydrozoans, ctenophores and pelagic tunicates. For these taxa, major knowledge gaps persist in their ecology, genetic structure and resilience to change. In both polar regions, Themisto’s genetic and trophic connectivity as well as thermal response were investigated with state-of-the-art molecular methods. The role of gelatinous zooplankton in the Arctic and Antarctic food webs is assessed with molecular diet studies. We also explore the genetic connectivity of dominant gelatinous species across the Arctic Ocean and its adjacent seas. Finally, we apply environmental DNA to detect incoming species into the vulnerable polar systems and aim to set the baseline for future monitoring efforts of gelatinous zooplankton communities.