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Abstract. Mesoscale eddies which origin in Eastern Boundary Upwelling Systems (EBUS) such as the Canary Current System entrap nutrient rich coastal water and travel offshore while ageing. We have analyzed the protistan plankton community structures in the deep chlorophyll maximum (DCM), sub-DCM and oxygen minimum zone (OMZ) of three differently aged cyclonic EBUS eddies off Northwest Africa as well as of non-eddy affected reference sites using DNA metabarcoding. Throughout all water depths, we found that the investigated eddies generated local dispersal-driven hotspots of protistan plankton diversity in the naturally oligotrophic subtropical offshore waters off Northwest Africa. Based on the taxonomic composition of protistan plankton communities, these diversity hotspots are likely to play an important role in carbon sequestration and for regional food webs up to top predatory levels. Thereby, the life-span of an eddy emerged as an important criterion, how local offshore protistan plankton diversity is transformed quantitatively and qualitatively: each of the three eddies was characterized by notably distinct protistan plankton communities. This could be linked to the physicochemical water properties (predominantly macronutrients, temperature and salinity) of the eddies’ cores and rings, which experience pronounced changes during the eddies’ westward trajectories. Furthermore, we found evidence that eddy-specific deep-water protistan communities are relatively short-lived compared to the ones in the sunlit DCM. However, our results do not only witness from the importance of fine-scale physical ocean features for regional ecosystem processes, but they also show the complexity of these ocean features and that we are still far from understanding the biological processes and their driving forces in such features.