The spatial and temporal variability in the fish component of the diet of Antarctic fur seals Arctocephalus gazella (Peters 1975) in the Atlantic sector of the Southern Ocean was examined using diet data from ten sites in the region including a 13 year time-series from South Georgia. The fish species composition in the diet at each site showed a strong relationship with the local marine habitat/topography. The absence of formerly harvested fish species indicates a lack of recovery of stocks of Notothenia rossii (Richardson 1844) at South Georgia and Champsocephalus gunnari (Lönnberg 1905) at the South Orkney Islands. At South Georgia Protomyctophum choriodon (Hulley 1981), Lepidonotothen larseni (Lönnberg 1905) and C.gunnari were the most important species in the diet between 1991 and 2004. Variability in the occurrence of the C. gunnari was driven mainly by annual scale processes, particularly those that influence the availability of Antarctic krill Euphausia superba (Dana 1852). The occurrence of the pelagic P. choriodon was primarily influenced by shorter-term water mass changes within the foraging range of the seals. The fish composition in the diet reflects differences in marine habitat/topography as well as variability at a range of time-scales that reflect environmental variability and harvesting.