The Filchner Outflow System (FOS) in the southern Weddell Sea is one of the most important areas for deep water formation. Here the outflow of Ice Shelf Water (ISW) of the Filchner Ronne Ice Shelf interacts with Warm Deep Water (WDW) of the Weddell Gyre circulation, resulting in Weddell Sea Deep and Bottom Water production (WSDW, WSBW). The interaction around the sill of the Filchner Trough is thought to result in a physical oceanography "hotspot" that may also aggregate primary and secondary producers, leading to increased abundance of top predators. However, data on top predator abundance for the FOS are scarce. Two aerial surveys over ice-covered sea were carried out to estimate density gradients and the regional abundance of pack ice seals in the FOS. A digital imaging survey with fixed wing research aircraft Polar 6 in November 2013 preceded a helicopter survey from aboard RV Polarstern during January 2014. The Polar 6 survey comprised 11 transects summing to a survey effort of 1,148.44 km. 265 seals were counted on transect lines with a higher encounter rate on transects located further to the west. The helicopter survey allowed seal species to be identified. Twenty-five transects (1,367.61 km) were flown in the FOS region and another six transects (425.54 km) further south within the Filchner Trough. Only two seal species, the crabeater seal (Lobodon carcinophaga) (n = 754) and the Weddell seal (Leptonychotes weddellii) (n = 217), were observed. Distance sampling analysis suggested that the density of seals differed strongly between the two survey regions, with very few seals encountered on transects located in the more southerly Filchner Trough region. A longitudinal density gradient increasing from east to west within the FOS region during January 2014 supported the results obtained from the Polar 6 survey, but failed to support the idea of a top predator hotspot at the sill of the Filchner Trough at least for seals.