Most of the iron fertilization experiments conducted in the Southern Ocean during the past two decades were carried out in high silicic acid waters and have induced phytoplankton blooms, dominated by diatoms. The iron fertilization experiment LOHAFEX, performed during the RV Polarstern cruise ANT XXV/3 from January to March 2009, was however carried out in a silicic acid depleted mesoscale eddy in the Atlantic sector of the Southern Ocean. The low silicic acid concentrations (<2 µM) limited diatom growth and the phytoplankton assemblage was instead dominated by nano- and picoeukaryotes. In the present study we used molecular methods to investigate the composition and succession of small phytoplankton (0.2-5µm) during LOHAFEX. This involves on the one hand ARISA (automated intergenic spacer analysis) and on the other hand 454 next generation sequencing. The ARISA approach is based on the heterogeneity of the region between the 18S and the 28S rRNA gene and delivers a quick community structure overview. The 454 sequencing is a high throughput approach and provides high resolution information on the phytoplankton diversity, including the rare biosphere. During LOHAFEX the 0.2-5µm phytoplankton fraction shows a high diversity. The most prominent classes are the Prasinophyceae (dominated by Micromonas pusilla), the Haptophyceae (dominated by Phaeocystis antarctica) and the Dinophyceae (dominated by Syndiniales). The fertilized and non-fertilized samples show a similar community structure and no significant differences concerning the abundance of the dominant species. In all samples there are a large number of sequences belonging to the rare biosphere. The results support the general notion that the diversity of the picoplankton community was highly underestimated in the past. There is still a vast number of unknown organisms, hiding in the rare biosphere, to discover. According to other studies, our outcome shows that in the northern part of the Southern Ocean the picoplankton assemblage is dominated by Micromonas pusilla and Phaeocystis antarctica. Measurements during the experiment revealed an increase in total biomass, attributed to the addition of iron. In our samples there is no species or group in the picoplankton community that is favored by the iron addition and the relative abundances remain constant. In conclusion the iron addition has increased picoplankton biomass but the assemblage composition did not change significantly.