The diet of Antarctic salps was elucidated by investigating their gut content using “Automated Ribosomal Intergenic Spacer Analysis” and 454-pyrosequencing. Salp samples were collected during the Lazarev Krill Study in the Western Weddell Sea (summer 2005/06 and 2007/08, fall 2004, and winter 2006). Two salp species, Salpa thompsoni and Ihlea racovitzai, both occur in the Southern Ocean, can overlap geographically and seasonally. Here we provide evidence that despite the non-selective feeding mechanism, the two co-occuring salp species might have different niches within one given habitat. ARISA-patterns of 93 salp gut content samples revealed strong differences between the two salp species, even at the same sampling site. These differences were confirmed by 454-pyrosequencing of the V4-18S rDNA of ten salps. The pyrosequencing data indicate that flagellates, in particular dinophyceae constitute a high proportion of the sequence reads identified in the gut content of both salp species. However, within the dinophyceae differences in the read composition were detected between the two salp species. This supports the findings of a previous study where fatty acid signatures indicate a flagellate based diet of salps, even though microscopic analyses identified diatoms as the dominant component of salp gut contents.