The spatial and temporal community composition of microzooplankton (dinoflagellates and ciliates) was assessed in the Kerguelen area (Southern Ocean) during the KEOPS2 cruise in early spring (October–November) 2011. This naturally iron-fertilized region was characterized by a complex mesoscale circulation resulting in a patchy distribution of phytoplankton blooms. Collectively, 97 morphospecies of dinoflagellates and ciliates belonging to 41 genera were identified by microscopy, and 202 Alveolata-related OTUs (operational taxonomical units) were retrieved with tag-pyrosequencing. Microscopy and pyrosequencing data were in accordance, in that diatom-consuming dinoflagellates were the most enhanced taxa in the blooms. Dinoflagellates also showed significant positive relationships with phytoplankton pigments, while no major differences were found in the ciliate abundances inside and outside the blooms. Cluster analysis showed clear differences in the phytoplankton and microzooplankton community structures between the iron-fertilized and HNLC (high nutrient low chlorophyll) waters, and between the blooms, concerning their location and the fertilization mechanisms. These results were combined with the rates of primary production and mesozooplankton consumption determined for the study area. The potential role of dinoflagellates and ciliates as phytoplankton consumers and as prey for mesozooplankton was then evaluated. Overall, heterotrophic dinoflagellates were probably the most important group of phytoplankton grazers, and a potential food source for copepods.