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Antarctic krill Euphausia superba are key components of Antarctic ecosystems, serving as the major prey item for most of the megafauna in the region. Coastal fjords along the West Antarctic Peninsula have been identified as biological hotspots, areas in which high biomasses of both E. superba and their megafauna predators are consistently observed. We investigated feeding by E. superba in fjords and adjacent open waters of the West Antarctic Peninsula. Next generation sequencing of stomach contents from 174 krill indicated a diverse diet, with broad patterns consistent with previous understanding of E. superba feeding. Diatom sequence reads were frequent and abundant, indicating a largely diatom-based diet, while the occasional presence of high abundances of copepod sequence reads suggests carnivory supplemented the diet. Striking differences were observed between the stomach contents of krill collected in fjords and those of krill collected in adjacent open waters. Chaetoceros spp. diatoms made up 71% of the stomach contents sequences of krill collected in fjords, but less than 10% of the stomach contents sequences of krill collected in open waters. These differences could not be explained by differences in the surface water phytoplankton communities, as in both open waters and fjords Chaetoceros spp. made up less than 10% of the surface water sequence read assemblages. These feeding differences highlight the importance of taking into account regional differences in krill feeding when considering E. superba’s roles in Southern Ocean ecosystems, and suggest krill in fjords may make use of vertical structure in phytoplankton assemblages.