Microzooplankton play an important role in aquatic food webs through their multiple interactions with other organisms and their impact on carbon export. They are major predators of phytoplankton and bacteria while being preyed on by higher trophic levels. Microzooplankton diversity (Dinoflagellates, DIN and Ciliates, CIL), community structure, interaction with phytoplankton and its potential in channeling carbon to higher trophic levels were studied in contrasting productivity regimes (off- and on-plateau, the latter been naturally fertilized by iron) around the Kerguelen islands in the Southern Ocean (SO). DIN and CIL diversity was sampled in late summer (February–March 2018; project MOBYDICK) and at the onset-of the bloom (KEOPS2 cruise), and assessed by Illumina sequencing of 18S rDNA amplicons and microscopic observations. The diversity obtained by the two approaches could be compared at a relatively high taxonomic level (i.e., often to family level). In particular for DIN, relative abundances and ranking of dominant taxa differed between sequencing and microscopy observations. CIL were always recorded at considerably lower abundances than DIN, the median of their abundances across stations and seasons being 350 and 1370 cells L−1, respectively. During late summer, DIN and CIL biomasses were about 1.5 times higher on- than in off-plateau waters, while community composition was spatially similar. The most abundant DIN at all stations and during both seasons were small Gymnodinium (<20 μm). During late summer, ciliates Lohmaniella oviformis (<20 μm) and Cymatocylis antarctica (20-40 μm) dominated on- and off-plateau, respectively. Dilution experiments suggested significant grazing of microzooplankton on phytoplankton as phytoplankton net growth (k) was lower than microzooplankton grazing (g) at all stations (mean k = 0.16 ± 0.05 d−1, g = 0.36 ± 0.09 d−1) in late summer. Despite having great potential as a phytoplankton grazer, microzooplankton occurred at low biomass and showed little temporal variability, suggesting that they were controlled by copepod predation. Microzooplankton are a key component of the SO as an intermediate trophic level mediating carbon transfer from primary producers to higher trophic levels.