<jats:title>Abstract</jats:title><jats:p>We determined the composition and structure of late summer eukaryotic protist assemblages along a west–east transect in the Amundsen Sea. We used state-of-the-art molecular approaches, such as automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing, combined with pigment measurements via high performance liquid chromatography (HPLC) to study the protist assemblage. We found characteristic offshore and inshore communities. In general, total chlorophyll <jats:italic>a</jats:italic> and microeukaryotic contribution were higher in inshore samples. Diatoms were the dominant group across the entire area, of which <jats:italic>Eucampia</jats:italic> sp. and <jats:italic>Pseudo-nitzschia</jats:italic> sp. were dominant inshore and <jats:italic>Chaetoceros</jats:italic> sp. was dominant offshore. At the most eastern station, the assemblage was dominated by <jats:italic>Phaeocystis</jats:italic> sp. Under the ice, ciliates showed their highest and haptophytes their lowest abundance. This study delivers a taxon detailed overview of the eukaryotic protist composition in the Amundsen Sea during the summer 2010.</jats:p>