Planktonic food webs were studied contemporaneously in a mesoscale cyclonic (upwelling, similar to 13 months old) and an anticyclonic (downwelling, similar to 2 months old) eddy as well as in an uninfluenced background situation in the oligotrophic southeastern Mediterranean Sea (SEMS) during late summer 2018. We show that integrated nutrient concentrations were higher in the cyclone compared to the anticyclone or the background stations by 2-13-fold. Concurrently, Synechococcus and Prochlorococcus were the dominant autotrophs abundance-wise in the oligotrophic anticyclone (similar to 300 x 10(10) cells m(-2)). In the cyclone, functional groups such as dinoflagellates, Prymnesiophyceae and Ochrophyta contributed substantially to the total phytoplankton abundance (similar to 14 x 10(10) cells m (-2) ), which was similar to 65 % lower at the anticyclone and background stations (similar to 5 x 10(10) cells m(-2)). Primary production was highest in the cyclonic eddy (191 mg C m(-2) d(-1)) and 2-5-fold lower outside the eddy area. Heterotrophic prokaryotic cell-specific activity was highest in the cyclone (similar to 10 fg C cell(-1) d(-1)), while the least productive cells were found in the anticyclone (4 fg C cell(-1) d(-1)). Total zooplankton biomass in the upper 300 m was 10-fold higher in the cyclone compared with the anticyclone or background stations (1337 vs. 112-133 mg C m(-2), respectively). Copepod diversity was much higher in the cyclone (44 species), compared to the anticyclone (6 small-size species). Our results highlight that cyclonic and anticyclonic eddies show significantly different community structure and food-web dynamics in oligotrophic environments, with cyclones representing productive oases in the marine desert of the SEMS.