In the Southern Ocean, diatom blooms have attracted a lot of attention, while other small nonsilicified phytoplankton groups have been less studied. Here, small phytoplankton (< 20 μ m, including small diatoms and nonsilicified small phytoplankton) are focused on in two contrasting areas: the productive Kerguelen plateau and its surrounding low productivity waters. To assess the diversity and spatial structuration of phytoplankton, discrete plankton samples (0–300 m layer) of two size fractions (< 20 and 20–100 μ m) were analyzed with 18S rDNA amplicon sequencing in late summer. Phytoplankton seasonal succession was described using flow cytometry, pigments, and environmental data, from two previous cruises (during the onset and decline of the diatom bloom). In the mixed layer, small nonsilicified phytoplankton represented less than 10% of chlorophyll a (Chl a ) during the onset and late diatom bloom on the plateau, but they increased on and off the plateau after the bloom (53–70% of Chl a ). Phaeocystis antarctica was relatively abundant at all stations after the bloom, but other small phytoplanktonic groups featured marked differences on and off the plateau. Higher concentrations on the plateau appeared to stimulate the presence of Micromonas , while Pelagophytes were enhanced off the plateau. A diverse assemblage of small diatoms was also promoted off the plateau, where silicate concentration was still high. Interestingly, P. antarctica represented up to 25% of all reads at 300 m depth off the plateau in the larger size fraction suggesting a significant contribution to carbon export through aggregation in low productive waters.