Rising water temperatures and ocean acidification are the major threats for polar marine ecosystems and will affect phytoplankton communities. Phytoplankton plays a major role in primary production and biogeochemical cycles and forms the basis of marine food webs. Changes in the composition and distribution of phytoplankton will affect the whole marine ecosystem. To assess the effects of changing environmental conditions on phytoplankton communities we have to know their current diversity and distribution. There is a lack of Phytoplankton diversity studies in the Pacific sector of the Southern Ocean, especially in the Amundsen Sea. To resolve this gap this study will deliver basic data of phytoplankton diversity and distribution, which will help identifying the dominant phytoplankton phyla and provide information on the rare biosphere in that area. Environmental samples, taken on the RV Polarstern cruise ANT XXVI/3, were analyzed with molecular approaches, including ARISA (automated ribosomal intergenic spacer analysis) and 454-pyrosequencing. Furthermore pigment analysis and flow cytometry were conducted. First results indicate a clustering of the samples according to the different water masses and regions with comparable environmental conditions. The sequencing will deliver more detailed information about the structure and diversity of phytoplankton in the Pacific sector of the Southern Ocean.