Abstract. Planktonic food-webs were studied contemporaneously in a mesoscale cyclonic (upwelling, ~13 months old) and an anti-cyclonic (down-welling, ~2 months old) eddies, as well as in an uninfluenced-background situation in the oligotrophic southeastern Mediterranean Sea (SEMS) during late summer 2018. We show that integrated nutrients concentrations were higher at the cyclone compared to the anti-cyclone or the background stations by 2–13 fold. Concurrently, Synechococcus and Prochlorococcus were the dominant community component abundance-wise in the oligotrophic anti-cyclone (~300 × 1010 cells m−2). In the cyclone, pico- and nanoeukaryotes such as dinoflagellates, Prymnesiophyceae and Ochrophyta contributed substantially to the total phytoplankton abundnce (~14 × 1010 cells m−2) which was ~65 % lower in the anti-cyclone/background stations (~5 × 1010 cells m−2). Primary production was highest in the cyclonic eddy (191 mg C m−2 d−1) and was 2–5 fold lower outside the eddy area. The calculated doubling time of phytoplankton was ~3 days in the cyclone and ~5–10 days at the anti-cyclone/background stations, further reflecting the nutritional differences between these environments. Heterotrophic prokaryotic cell-specific activity was highest in the cyclone (~10 fg C cell−1 d−1), while the least productive cells were found in the anti-cyclone (4 fg C cell−1 d−1). The calculated doubling time of heterotrophic bacteria were 1.4 days in the cyclone and 2.5–3.5 days at the anti-cyclone/background stations. Total zooplankton biomass in the upper 300 m was tenfold higher in the cyclone compared with the anti-cyclone 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 anti-cyclone (6 small-size species). Our results highlight that cyclonic and anti-cyclonic eddies show significantly different community compositions and food-web dynamics in oligotrophic environments, with cyclones representing productive oases in the marine desert of the SEMS.